Mercurial > repos > iuc > arriba
changeset 0:a24ca22b906e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
| author | iuc |
|---|---|
| date | Wed, 27 Jul 2022 11:24:44 +0000 |
| parents | |
| children | 4f1efcc055d5 |
| files | arriba.xml macros.xml static/images/draw-fusions-example.png test-data/Aligned.out.bam test-data/Aligned.out.bam.bai test-data/Aligned.out.sam test-data/cytobands.tsv test-data/fusions.tsv test-data/genome.fasta.gz test-data/genome.gtf.gz test-data/protein_domains.gff3 tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 13 files changed, 1272 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba.xml Wed Jul 27 11:24:44 2022 +0000 @@ -0,0 +1,757 @@ +<tool id="arriba" name="Arriba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> + <description>detect gene fusions from STAR aligned RNA-Seq data</description> + <macros> + <import>macros.xml</import> + <xml name="fusion_actions"> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="gene1,gene2,strand1(gene/fusion),strand2(gene/fusion),breakpoint1,breakpoint2,site1,site2,type,split_reads1,split_reads2,discordant_mates,coverage1,coverage2,confidence,reading_frame,tags,retained_protein_domains,closest_genomic_breakpoint1,closest_genomic_breakpoint2,gene_id1,gene_id2,transcript_id1,transcript_id2,direction1,direction2,filters,fusion_transcript,peptide_sequence,read_identifiers" /> + </actions> + </xml> + <token name="@VIRAL_CONTIG@">([AN]C_([*]|\d+))</token> + <token name="@GENOME_CONTIG@">((chr)?(\d|\d\d|X|Y|M(t)?))</token> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ +@GENOME_SOURCE@ +@GTF_SOURCE@ +#set $filter_list = [] +#if $options.filters + #set $filter_list = $options.filters.split(',') +#end if +#if $blacklist + #if $blacklist.is_of_type('tabular.gz') + #set $blacklist_file = 'blacklist.tsv.gz' + ln -sf '$blacklist' $blacklist_file && + #else + #set $blacklist_file = $blacklist + #end if +#else + #if 'blacklist' not in $filter_list + #silent $filter_list.append('blacklist') + #end if +#end if +#set $filters = ','.join($filter_list) +#if $known_fusions + #if $known_fusions.is_of_type('tabular.gz') + #set $known_fusions_file = 'known_fusions.tsv.gz' + ln -sf '$known_fusions' $known_fusions_file && + #else + #set $known_fusions_file = $known_fusions + #end if +#end if +#if $tags + #if $tags.is_of_type('tabular.gz') + #set $tags_file = 'tags.tsv.gz' + ln -sf '$tags' $tags_file && + #else + #set $tags_file = $tags + #end if +#end if + arriba + -x '$input' + #if $chimeric + -c '$chimeric' + #end if + -a '$genome_assembly' + -g '$genome_annotation' + #if $blacklist + -b '$blacklist_file' + #end if + #if $filters + -f '$filters' + #end if + #if $protein_domains + -p '$protein_domains' + #end if + #if $known_fusions + -k '$known_fusions_file' + #end if + #if $tags + -t '$tags_file' + #end if + #if str($wgs.use_wgs) == "yes" + -d '$wgs.wgs' + #if str($wgs.max_genomic_breakpoint_distance) + -D $wgs.max_genomic_breakpoint_distance + #end if + #end if + -o fusions.tsv +#if $output_fusions_discarded + -O fusions.discarded.tsv +#end if +## Arriba options + #if $options.gtf_features + -G '$options.gtf_features' + #end if + #if $options.strandedness + -s $options.strandedness + #end if + #if $options.genome_contigs + -i '$options.genome_contigs' + #end if + #if $options.viral_contigs + -v '$options.viral_contigs' + #end if + #if str($options.max_evalue) + -E $options.max_evalue + #end if + #if str($options.min_supporting_reads) + -S $options.min_supporting_reads + #end if + #if str($options.max_mismappers) + -m $options.max_mismappers + #end if + #if str($options.max_homolog_identity) + -L $options.max_homolog_identity + #end if + #if str($options.homopolymer_length) + -H $options.homopolymer_length + #end if + #if str($options.read_through_distance) + -R $options.read_through_distance + #end if + #if str($options.min_anchor_length) + -A $options.min_anchor_length + #end if + #if str($options.many_spliced_events) + -M $options.many_spliced_events + #end if + #if str($options.max_kmer_content) + -K $options.max_kmer_content + #end if + #if str($options.max_mismatch_pvalue) + -V $options.max_mismatch_pvalue + #end if + #if str($options.fragment_length) + -F $options.fragment_length + #end if + #if str($options.max_reads) + -U $options.max_reads + #end if + #if $options.quantile + -Q $options.quantile + #end if + #if str($options.exonic_fraction) + -e $options.exonic_fraction + #end if + #if str($options.top_n) + -T $options.top_n + #end if + #if str($options.covered_fraction) + -C $options.covered_fraction + #end if + #if str($options.max_itd_length) + -l $options.max_itd_length + #end if + #if str($options.min_itd_allele_fraction) + -z $options.min_itd_allele_fraction + #end if + #if str($options.min_itd_supporting_reads) + -Z $options.min_itd_supporting_reads + #end if + $options.duplicate_marking + $options.fill_discarded_columns + $options.fill_the_gaps +#if str($visualization.do_viz) == "yes" + && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam + && samtools index Aligned.sortedByCoord.out.bam +#end if +#if $output_fusions_vcf + && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf +#end if +#if $output_fusion_bams + && mkdir fusion_bams + && extract_fusion-supporting_alignments.sh fusions.tsv Aligned.sortedByCoord.out.bam 'fusion_bams/fusion' +#end if +#if str($visualization.do_viz) == "yes" + #set $fusions = 'fusions.tsv' + && @DRAW_FUSIONS@ +#end if + ]]></command> + <inputs> + <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"> + <help><![CDATA[ recommended STAR options: --chimSegmentMin 10 --chimOutType WithinBAM ]]></help> + </param> + <param name="chimeric" argument="-c" type="data" format="sam,bam,cram" optional="true" label="STAR Chimeric.out.sam"> + <help><![CDATA[ only required, if STAR was run with the parameter '--chimOutType SeparateSAMold' ]]></help> + </param> + <expand macro="genome_source" /> + <expand macro="gtf_source" /> + <param name="blacklist" argument="-b" type="data" format="tabular,tabular.gz" optional="true" label="File containing blacklisted ranges."/> + <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/> + <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz" optional="true" label="File containing known fusions"> + <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help> + </param> + <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion." + help="This can be the known fusions if that input has a third column with a name"/> + <conditional name="wgs"> + <param name="use_wgs" type="select" label="Use whole-genome sequencing data"> + <option value="no">no</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="wgs" argument="-d" type="data" format="tabular" label="whole-genome sequencing structural variant data" + help="These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence."/> + <param name="max_genomic_breakpoint_distance" argument="-D" type="integer" value="100000" min="0" label="Max genomic breakpoint distance" + help="determines how far a genomic breakpoint may be away from a transcriptomic breakpoint to consider it as a related event."/> + </when> + <when value="no"/> + </conditional> + <section name="options" expanded="false" title="Arriba Options"> + <param name="gtf_features" argument="-G" type="text" value="" optional="true" label="Names of features in the GTF annotation file"> + <help>Commma or SPACE separated list, default: gene_name=gene_name|gene_id gene_id=gene_id transcript_id=transcript_id feature_exon=exon feature_CDS=CDS</help> + <validator type="regex" message="">^(gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=\w+(|\w+)?([ ,](gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=\w+(|\w+)?)*$</validator> + </param> + <param name="strandedness" argument="-s" type="select" optional="true" label="Whether a strand-specific protocol was used for library preparation"> + <help>When unstranded data is processed, the strand can sometimes be inferred from splice-patterns. But in unclear situations, stranded data helps resolve ambiguities.</help> + <option value="auto">auto</option> + <option value="yes">yes</option> + <option value="no">no</option> + <option value="reverse">reverse</option> + </param> + <param name="genome_contigs" argument="-i" type="text" value="" optional="true" label="Comma/space-separated list of interesting contigs"> + <help>Comma-/space-separated list of interesting contigs. + Fusions between genes on other contigs are ignored. Contigs can be specified with or without the prefix "chr". + Asterisks (*) are treated as wild-cards. + Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_* + </help> + <validator type="regex" message="not a valid contig name">^((@GENOME_CONTIG@|@VIRAL_CONTIG@)([,\s]\s*(*@GENOME_CONTIG@|@VIRAL_CONTIG@))*)*</validator> + </param> + <param name="viral_contigs" argument="-v" type="text" value="" optional="true" label="Comma/space-separated list of viral contigs"> + <help>Comma-/space-separated list of viral contigs for reporting of viral integration sites. + Asterisks (*) are treated as wild-cards. + Default: AC_* NC_* + </help> + <validator type="regex" message="not a valid contig name">^(@VIRAL_CONTIG@([,\s]\s*@VIRAL_CONTIG@)*)*$</validator> + </param> + <param name="filters" argument="-f" type="select" optional="true" multiple="true" label="Disable filters"> + <help>By default all filters are enabled.</help> + <option value="top_expressed_viral_contigs">top_expressed_viral_contigs</option> + <option value="viral_contigs">viral_contigs</option> + <option value="low_coverage_viral_contigs">low_coverage_viral_contigs</option> + <option value="uninteresting_contigs">uninteresting_contigs</option> + <option value="no_genomic_support">no_genomic_support</option> + <option value="short_anchor">short_anchor</option> + <option value="select_best">select_best</option> + <option value="many_spliced">many_spliced</option> + <option value="long_gap">long_gap</option> + <option value="merge_adjacent">merge_adjacent</option> + <option value="hairpin">hairpin</option> + <option value="small_insert_size">small_insert_size</option> + <option value="same_gene">same_gene</option> + <option value="genomic_support">genomic_support</option> + <option value="read_through">read_through</option> + <option value="no_coverage">no_coverage</option> + <option value="mismatches">mismatches</option> + <option value="homopolymer">homopolymer</option> + <option value="low_entropy">low_entropy</option> + <option value="multimappers">multimappers</option> + <option value="inconsistently_clipped">inconsistently_clipped</option> + <option value="duplicates">duplicates</option> + <option value="homologs">homologs</option> + <option value="blacklist">blacklist</option> + <option value="mismappers">mismappers</option> + <option value="spliced">spliced</option> + <option value="relative_support">relative_support</option> + <option value="min_support">min_support</option> + <option value="known_fusions">known_fusions</option> + <option value="end_to_end">end_to_end</option> + <option value="non_coding_neighbors">non_coding_neighbors</option> + <option value="isoforms">isoforms</option> + <option value="intronic">intronic</option> + <option value="in_vitro">in_vitro</option> + <option value="intragenic_exonic">intragenic_exonic</option> + <option value="internal_tandem_duplication">internal_tandem_duplication</option> + </param> + + <param name="max_evalue" argument="-E" type="float" value="" min="0" optional="true" label="Max e-value threshold"> + <help>Arriba estimates the number of fusions with a given number of supporting + reads which one would expect to see by random chance. If the expected number + of fusions (e-value) is higher than this threshold, the fusion is + discarded by the 'relative_support' filter. Note: Increasing this + threshold can dramatically increase the number of false positives and may + increase the runtime of resource-intensive steps. Fractional values are possible. + Default: 0.300000 + </help> + </param> + + <param name="min_supporting_reads" argument="-S" type="integer" value="" min="1" optional="true" label="Min supporting reads"> + <help>discard all fusions with fewer than this many supporting reads (split reads and discordant mates combined). + Default: 2 + </help> + </param> + <param name="max_mismappers" argument="-m" type="float" value="" min="0." max="1.0" optional="true" label="Max mismappers threshold"> + <help>When more than this fraction of supporting reads turns out to be mismappers, + the 'mismappers' filter discards the fusion. + Default: 0.800000 + </help> + </param> + <param name="max_homolog_identity" argument="-L" type="float" value="" min="0." max="1.0" optional="true" label="Max homologs identity threshold"> + <help>Genes with more than the given fraction of sequence identity are + considered homologs and removed by the 'homologs' filter. + Default: 0.300000 + </help> + </param> + <param name="homopolymer_length" argument="-H" type="integer" value="" min="1" optional="true" label="Homopolymer length"> + <help>The 'homopolymer' filter removes breakpoints adjacent to homopolymers of the given length or more. + Default: 6 + </help> + </param> + <param name="read_through_distance" argument="-R" type="integer" value="" min="1" optional="true" label="Read-through distance"> + <help>The 'read_through' filter removes read-through fusions + where the breakpoints are less than the given distance away from each other. + Default: 10000 + </help> + </param> + <param name="min_anchor_length" argument="-A" type="integer" value="" min="1" optional="true" label="Min anchor length"> + <help>Alignment artifacts are often characterized by split reads coming + from only one gene and no discordant mates. Moreover, the split + reads only align to a short stretch in one of the genes. The + 'short_anchor' filter removes these fusions. This parameter sets + the threshold in bp for what the filter considers short. + Default: 23 + </help> + </param> + <param name="many_spliced_events" argument="-M" type="integer" value="" min="1" optional="true" label="Many spliced events"> + <help>The 'many_spliced' filter recovers fusions between genes that + have at least this many spliced breakpoints. + Default: 4 + </help> + </param> + <param name="max_kmer_content" argument="-K" type="float" value="" min="0." max="1.0" optional="true" label="Max kmer content"> + <help>The 'low_entropy' filter removes reads with repetitive 3-mers. If + the 3-mers make up more than the given fraction of the sequence, then + the read is discarded. + Default: 0.600000 + </help> + </param> + + <param name="max_mismatch_pvalue" argument="-V" type="float" value="" min="0." max="1." optional="true" label="Max mismatchrpvalue threahold"> + <help>The 'mismatches' filter uses a binomial model to calculate a + p-value for observing a given number of mismatches in a read. + If the number of mismatches is too high, the read is discarded. + Default: 0.010000 + </help> + </param> + + <param name="fragment_length" argument="-F" type="integer" value="" min="1" optional="true" label="Single-end fragment length"> + <help>When paired-end data is given, the fragment length is estimated + automatically and this parameter has no effect. But when single-end + data is given, the mean fragment length should be specified to + effectively filter fusions that arise from hairpin structures. + Default: 200 + </help> + </param> + <param name="max_reads" argument="-U" type="integer" value="" min="1" optional="true" label="Max reads"> + <help>Subsample fusions with more than the given number of supporting reads. This + improves performance without compromising sensitivity, as long as the + threshold is high. Counting of supporting reads beyond the threshold is + inaccurate, obviously. + Default: 300 + </help> + </param> + <param name="quantile" argument="-Q" type="float" value="" min="0." max="1.0" optional="true" label="Quantile"> + <help>Highly expressed genes are prone to produce artifacts during library preparation. + Genes with an expression above the given quantile are eligible for filtering by the 'in_vitro' filter. + Default: 0.998000 + </help> + </param> + <param name="exonic_fraction" argument="-e" type="float" value="" min="0." max="1.0" optional="true" label="Exonic fraction"> + <help>The breakpoints of false-positive predictions of intragenic events + are often both in exons. True predictions are more likely to have at + least one breakpoint in an intron, because introns are larger. + If the fraction of exonic sequence between two breakpoints is smaller than + the given fraction, the 'intragenic_exonic' filter discards the event. + Default: 0.330000 + </help> + </param> + + <param name="top_n" argument="-T" type="integer" value="" min="1" optional="true" label="top N viral contigs"> + <help>Only report viral integration sites of the top N most highly expressed viral contigs. + Default: 5 + </help> + </param> + <param name="covered_fraction" argument="-C" type="float" value="" min="0." max="1.0" optional="true" label="Covered fraction"> + <help>Ignore virally associated events if the virus is not fully expressed, + i.e., less than the given fraction of the viral contig is transcribed. + Default: 0.050000 + </help> + </param> + <param name="max_itd_length" argument="-l" type="integer" value="" min="1" optional="true" label="Maximum length of internal tandem duplications"> + <help>Note: Increasing this value beyond the default can impair performance and lead to many false positives. + Default: 100 + </help> + </param> + <param name="min_itd_allele_fraction" argument="-z" type="float" value="" min="0." max="1.0" optional="true" label="Required fraction of supporting reads to report an internal tandem duplication"> + <help> Default: 0.070000 + </help> + </param> + <param name="min_itd_supporting_reads" argument="-Z" type="integer" value="" min="1" optional="true" label="Required number of supporting reads to report an internal tandem duplication"> + <help> Default: 10 + </help> + </param> + <param name="duplicate_marking" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Use aligners duplicate marking"> + <help>Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a + preceding program using the BAM_FDUP flag. This makes sense when unique molecular + identifiers (UMI) are used. + </help> + </param> + <param name="fill_discarded_columns" argument="-X" type="boolean" truevalue="-X" falsevalue="" checked="false" label="Fill all fusion.discarded.tsv columns"> + <help>To reduce the runtime and file size, by default, the columns 'fusion_transcript', + 'peptide_sequence', and 'read_identifiers' are left empty in the file containing + discarded fusion candidates (see parameter -O). When this flag is set, this extra + information is reported in the discarded fusions file. + </help> + </param> + <param name="fill_the_gaps" argument="-I" type="boolean" truevalue="-I" falsevalue="" checked="false" label="Fill fusion transcript gaps from the assembly"> + <help>If assembly of the fusion transcript sequence from the supporting reads is incomplete + (denoted as '...'), fill the gaps using the assembly sequence wherever possible. + </help> + </param> + </section> + <param name="output_fusions_discarded" argument="-O" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.discarded.tsv"/> + <param name="output_fusions_vcf" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.vcf"/> + <param name="output_fusion_bams" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output fusion BAMs"/> + <conditional name="visualization"> + <param name="do_viz" type="select" label="Generate visualization"> + <option value="yes">Yes</option> + <option value="no">no</option> + </param> + <when value="yes"> + <expand macro="visualization_options" /> + </when> + <when value="no"/> + </conditional> + </inputs> + <outputs> + <data name="fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"> + <expand macro="fusion_actions" /> + </data> + + <data name="discarded_fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"> + <filter> output_fusions_discarded == True</filter> + <expand macro="fusion_actions" /> + </data> + <data name="fusions_vcf" format="vcf" label="${tool.name} on ${on_string}: fusions.vcf" from_work_dir="fusions.vcf"> + <filter> output_fusions_vcf == True</filter> + </data> + <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments"> + <discover_datasets pattern="(?P<name>fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/> + <filter>output_fusion_bams == True</filter> + </collection> + <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> + <filter>input_params['input_source'] == "use_fastq"</filter> + </data> + <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> + <filter>visualization['do_viz'] == "yes"</filter> + </data> + </outputs> + <tests> + <!-- Test 1 - From exisitng BAM --> + <test> + <param name="input" ftype="sam" value="Aligned.out.sam"/> + <conditional name="genome"> + <param name="genome_source" value="history"/> + <param name="assembly" ftype="fasta" value="genome.fasta.gz"/> + </conditional> + <conditional name="genome_gtf"> + <param name="gtf_source" value="history"/> + <param name="annotation" ftype="gtf" value="genome.gtf.gz"/> + </conditional> + <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> + <conditional name="visualization"> + <param name="do_viz" value="no"/> + <param name="cytobands" ftype="tabular" value="cytobands.tsv"/> + </conditional> + <output name="fusions_tsv"> + <assert_contents> + <has_text_matching expression="BCR\tABL1"/> + </assert_contents> + </output> + </test> + <!-- Test 2 - From exisitng BAM with protein_domains and visualization --> + <test> + <param name="input" ftype="sam" value="Aligned.out.sam"/> + <conditional name="genome"> + <param name="genome_source" value="history"/> + <param name="assembly" ftype="fasta" value="genome.fasta.gz"/> + </conditional> + <conditional name="genome_gtf"> + <param name="gtf_source" value="history"/> + <param name="annotation" ftype="gtf" value="genome.gtf.gz"/> + </conditional> + <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> + <conditional name="visualization"> + <param name="do_viz" value="yes"/> + <param name="cytobands" ftype="tabular" value="cytobands.tsv"/> + </conditional> + <output name="fusions_tsv"> + <assert_contents> + <has_text_matching expression="BCR\tABL1"/> + </assert_contents> + </output> + <output name="fusions_pdf"> + <assert_contents> + <has_size value= "64000" delta="5000" /> + </assert_contents> + </output> + </test> + + </tests> + <help><![CDATA[ +**Arriba** + + +Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. +It is based on chimeric alignments found by the STAR RNA-Seq aligner. + + +**INPUTS** + +See: https://arriba.readthedocs.io/en/latest/input-files/ + + - Alignments + + Arriba takes the main output file of STAR (Aligned.out.bam) as input (parameter -x). If STAR was run with the parameter --chimOutType WithinBAM, then this file contains all the information needed by Arriba to find fusions. When STAR was run with the parameter --chimOutType SeparateSAMold, the main output file lacks chimeric alignments. Instead, STAR writes them to a separate output file named Chimeric.out.sam. In this case, the file needs to be passed to Arriba via the parameter -c in addition to the main output file Aligned.out.bam. + + STAR index create recommended parameter value: + + * --sjdbOverhang 250 + + + STAR recommended parameter values :: + + * --outSAMunmapped Within + * --outFilterMultimapNmax 50 + * --peOverlapNbasesMin 10 + * --alignSplicedMateMapLminOverLmate 0.5 + * --alignSJstitchMismatchNmax 5 -1 5 5 + * --chimSegmentMin 10 + * --chimOutType WithinBAM HardClip + * --chimJunctionOverhangMin 10 + * --chimScoreDropMax 30 + * --chimScoreJunctionNonGTAG 0 + * --chimScoreSeparation 1 + * --chimSegmentReadGapMax 3 + * --chimMultimapNmax 50 + + + Arriba extracts three types of reads from the alignment file(s): + + * Split-reads, i.e., reads composed of segments which map in a non-linear way. STAR stores such reads as supplementary alignments. + * Discordant mates, i.e., paired-end reads which originate from the same fragment but which align in a non-linear way. + * Alignments which cross the boundaries of annotated genes, because these alignments might arise from focal deletions. In RNA-Seq data deletions of up to several hundred kb are hard to distinguish from splicing. They are represented identically as gapped alignments, because the sizes of many introns are in fact of this order of magnitude. STAR applies a rather arbitrary measure to decide whether a gapped alignment arises from splicing or from a genomic deletion: The parameter --alignIntronMax determines what gap size is still assumed to be a splicing event and introns are used to represent these gaps. Only gaps larger than this limit are classified as potential evidence for genomic deletions and are stored as chimeric alignments. Most STAR-based fusion detection tools only consider chimeric alignments as evidence for gene fusions and are blind to focal deletions, hence. As a workaround, these tools recommend reducing the value of the parameter --alignIntronMax. But this impairs the quality of alignment, because it reduces the scope that STAR searches to find a spliced alignment. To avoid compromising the quality of alignment for the sake of fusion detection, the only solution would be to run STAR twice - once with settings optimized for regular alignment and once for fusion detection. This would double the runtime. In contrast, Arriba does not require to reduce the maximum intron size. It employs a more sensible criterion to distinguish splicing from deletions: Arriba considers all those reads as potential evidence for deletions that span the boundary of annotated genes. + + The alignment files can be in SAM, BAM, and CRAM format. They need not be sorted for Arriba to accept them, but doing so comes with benefits: Often, this reduces the file size. And more importantly, the supporting reads of a fusion can be inspected visually using a genome browser like IGV, which typically requires BAM files to be sorted by coordinate. + + Single-end and paired-end data and even mixtures are supported. Arriba automatically determines the data type on a read-by-read basis using the flag BAM_FPAIRED. + + + - Assembly + + Arriba takes the assembly as input (parameter -a) to find mismatches between the chimeric reads and the reference genome, as well as to find alignment artifacts and homologous genes. + + The script download_references.sh can be used to download the assembly. The available assemblies are listed when the script is run without parameters. The user is not restricted to these assemblies, however. Any assembly can be used as long as its coordinates are compatible with one of the supported assemblies (hg19/hs37d5/GRCh37 or hg38/GRCh38 or mm10/GRCm38). + + The assembly must be provided in FastA format and may be gzip-compressed. An index with the file extension .fai must exist only if CRAM files are processed. + + - Annotation + + The gene annotation (parameter -g) is used for multiple purposes: + + annotation of breakpoints with genes + increased sensitivity for breakpoints at splice-sites + calculation of transcriptomic distances + determining the putative orientation of fused genes (i.e., 5' and 3' end) + GENCODE annotation is recommended over RefSeq annotation, because the former has a more comprehensive annotation of transcripts and splice-sites, which boosts the sensitivity. The file must be provided in GTF format and may be gzip-compressed. It does not need to be sorted. + + The script download_references.sh can be used to download the annotation. The available annotation files are listed when the script is run without parameters. The user is not restricted to these annotation files, however. Any annotation can be used as long as its coordinates are compatible with one of the supported assemblies (hg19/hs37d5/GRCh37 or hg38/GRCh38 or mm10/GRCm38). + + + - Blacklist + + It is strongly advised to run Arriba with a blacklist (parameter -b). Otherwise, the false positive rate increases by an order of magnitude. For this reason, using Arriba with assemblies or organisms which are not officially supported is not recommended. At the moment, the supported assemblies are: hg19/hs37d5/GRCh37, hg38/GRCh38, and mm10/GRCm38 (as well as any other assemblies that have compatible coordinates). The blacklists are contained in the release tarballs of Arriba. + + The blacklist removes recurrent alignment artifacts and transcripts which are present in healthy tissue. This helps eliminate frequently observed transcripts, such as read-through fusions between neighboring genes, circular RNAs and other non-canonically spliced transcripts. It was trained on RNA-Seq samples from the Human Protein Atlas, the Illumina Human BodyMap2 , the ENCODE project , the Roadmap Epigenomics project, and the NCT MASTER cohort, a heterogeneous cohort of cancer samples, from which highly recurrent artifacts were identified. + + Blacklists for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/blacklist_*. + + The blacklist is a tab-separated file with two columns and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions between which events are ignored. A region can be: + * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). If CONTIG ends on an asterisk (*), the contig with the closest matching name is chosen. + * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000). + * the name of a gene given in the provided annotation. + + In addition, special keywords are allowed for the second column: + * any: Discard all events if one of the breakpoints matches the given region. + * split_read_donor: Discard fusions only supported by split reads, if all of them have their anchor in the gene given in the first column. This filter is useful for highly mutable loci, which frequently trigger clipped alignments, such as the immunoglobulin loci or the T-cell receptor loci. + * split_read_acceptor: Discard events only supported by split reads, if all of them have their clipped segment in the given region. + * split_read_any: Discard events only supported by split reads, regardless of where the anchor is. + * discordant_mates: Discard fusions, if they are only supported by discordant mates (no split reads). + * low_support: Discard events, which have few supporting reads relative to expression (as determined by the filter relative_support), even if there is other evidence that the fusion might be a true positive, nonetheless. This keyword effectively prevents recovery of speculative events by filters such as spliced or many_spliced. + * filter_spliced: This keyword prevents the filter spliced from being applied to a given region. It is triggered under the same circumstances as the keyword low_support, but additionally requires that the breakpoints be at splice-sites for the event to be discarded. Some breakpoints produce recurrent artifacts, but the second breakpoint is always a different one, such that the pair of breakpoints is not recurrent and cannot be blacklisted. Often, such breakpoints are at splice-sites and the filter spliced tends to recover them. This keyword prevents the filter from doing so. + * not_both_spliced: This keyword discards events, unless both breakpoints are at splice-sites. This is a strict blacklist criterion, which makes sense to apply to genes which are prone to produce artifacts, because they are highly expressed, for example hemoglobins, collagens, or ribosomal genes. + * read_through: This keyword discards events, if they could arise from read-through transcription, i.e., the supporting reads are oriented like a deletion and are at most 400 kb apart. + + + - Known fusions + + Arriba can be instructed to be particularly sensitive towards events between certain gene pairs by supplying a list of gene pairs (parameter -k). A number of filters are not applied to these gene pairs. This is useful to improve the detection rate of expected or highly relevant events, such as recurrent fusions. Occassionally, this leads to false positive calls. But if high sensitivity is more important than specificity, this might be acceptable. Events which would be discarded by a filter and were recovered due to being listed in the known fusions list are usually assigned a low confidence. + + Known fusions files for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/known_fusions_*. + + The file has two columns separated by a tab and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions to which very sensitive filtering thresholds are applied. A region can be: + + * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). If CONTIG ends on an asterisk (*), the contig with the closest matching name is chosen. + * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000). + * the name of a gene given in the provided annotation. + + The order of the given regions is important. The region given in the first column is assumed to denote the 5' end of the fusion and the region in the second column to be the 3' end. If Arriba cannot determine with confidence which gene constitutes the 5' and which the 3' end of a fusion prediction, then the order is ignored and the prediction is rescued in both cases. + + + - Tags + + Arriba can be supplied with a list of user-defined tags using the parameter -t. Whenever a fusion prediction matches the selection criteria for a tag, the column tags is populated with the respective tag. This feature is useful to annotate known oncogenic fusions, for example. + + The known fusions file shipped with the download package of Arriba can be used for both known fusions and tags. It is constructed in a way that it can be passed as arguments to the parameters -k and -t alike. The former only uses the first two columns, the latter uses all three columns. If a user wants to separate filtering of known fusions and tagging of interesting fusions, different files may be used, however. + + The file has three columns separated by a tab and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions to be annotated. The first two columns specify the regions to be annotated; the third column the tag that is used for annotation. Some special characters in the tag are replaced with underscores (_) in Arriba's output file. A region can be: + + * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). + * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000). + * the name of a gene given in the provided annotation. + + The order of the given regions is important. The region given in the first column is assumed to denote the 5' end of the fusion and the region in the second column to be the 3' end. + + - Protein domains + + Protein domain annotation can be passed to Arriba via the parameter -p. The column retained_protein_domains of Arriba's output file is then populated accordingly. + + Protein domain annotation files for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/protein_domains_*. + + The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes: + * Name=PROTEIN_DOMAIN_NAME; + * gene_id=GENE_ID; + * gene_name=GENE_NAME + + The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs. + + - Structural variant calls from WGS + + If whole-genome sequencing (WGS) data is available, the sensitivity and specificity of Arriba can be improved by passing a list of structural variants detected from WGS to Arriba via the parameter -d. This has the following effects: + + Certain filters are overruled or run with extra sensitive settings, when an event is confirmed by WGS data. + To reduce the false positive rate, Arriba does not report low-confidence events unless they can be matched with a structural variant found in the WGS data. + Both of these behaviors can be disabled by disabling the filters genomic_support and no_genomic_support, respectively. Providing Arriba with a list of structural variant calls then does not influence the calls, but it still has the benefit of filling the columns closest_genomic_breakpoint1 and closest_genomic_breakpoint2 with the breakpoints of the structural variant which is closest to a fusion. If the structural variant calls were obtained from whole-exome sequencing (WES) data rather than WGS data, the filter no_genomic_support should be disabled, since WES has poor coverage in most regions of the genome, such that many structural variants are missed. + + Two file formats are accepted: a simple four-column format and the standard Variant Call Format (VCF). The format is detected automatically. + + * In case of the simple format, the file must contain four columns separated by tabs. The first two columns contain the breakpoints of the structural variants in the format CONTIG:POSITION. The last two columns contain the orientation of the breakpoints. The accepted values are: + + + downstream or +: the fusion partner is fused downstream of the breakpoint, i.e., at a coordinate higher than the breakpoint + + upstream or -: the fusion partner is fused at a coordinate lower than the breakpoint + + Example: + + :: + + =========== =========== =========== =========== + 5-prime 3-prime orientation orientation + =========== =========== =========== =========== + 1:54420491 6:9248349 + - + 20:46703288 20:46734546 - + + 17:61499820 20:45133874 + + + 3:190967119 7:77868317 - - + =========== =========== =========== =========== + + + * In case of the Variant Call Format, the file must comply with the VCF specification for structural variants. In particular, Arriba requires that the SVTYPE field be present in the INFO column and specify one of the four values BND, DEL, DUP, INV. In addition, for all SVTYPEs other than BND, the END field must be present and specify the second breakpoint of the structural variant. Structural variants with single breakends are silently ignored. + + Arriba checks if the orientation of the structural variant matches that of a fusion detected in the RNA-Seq data. If, for example, Arriba predicts the 5' end of a gene to be retained in a fusion, then a structural variant is expected to confirm this, or else the variant is not considered to be related. + + NOTE: Arriba was designed for alignments from RNA-Seq data. It should not be run on WGS data directly. Many assumptions made by Arriba about the data (statistical models, blacklist, etc.) only apply to RNA-Seq data and are not valid for DNA-Seq data. For such data, a structural variant calling algorithm should be used and the results should be passed to Arriba. + + +**OPTIONS** + + - Arriba: https://arriba.readthedocs.io/en/latest/command-line-options/#arriba + - Visualization: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr + - RNA STAR: https://arriba.readthedocs.io/en/latest/workflow/ + + +**OUTPUTS** + +See: https://arriba.readthedocs.io/en/latest/output-files/ + + - fusions.tsv + + The file fusions.tsv (as specified by the parameter -o) contains fusions which pass all of Arriba's filters. It should be highly enriched for true predictions. The predictions are listed from highest to lowest confidence. The following paragraphs describe the columns in detail: + + * gene1 and gene2 : gene1 contains the gene which makes up the 5' end of the transcript and gene2 the gene which makes up the 3' end. The order is predicted on the basis of the strands that the supporting reads map to, how the reads are oriented, and splice patterns. Both columns may contain the same gene, if the event is intragenic. If a breakpoint is in an intergenic region, Arriba lists the closest genes upstream and downstream from the breakpoint, separated by a comma. The numbers in parentheses after the closest genes state the distance to the genes. If no genes are annotated for a contig (e.g., for viral genomes), the column contains a dot (.). + + * strand1(gene/fusion) and strand2(gene/fusion) : Each of these columns contains two values seperated by a slash. The strand before the slash reflects the strand of the gene according to the gene annotation supplied to Arriba via the parameter -g. If the breakpoint is in an intergenic region, the value is .. The value after the slash reflects the strand that is transcribed. This does not necessarily match the strand of the gene, namely when the sense strand of a gene serves as the template for transcription. Occassionally, the strand that is transcribed cannot be predicted reliably. In this case, Arriba indicates the lack of information as a dot (.). Arriba uses splice-patterns of the alignments to assign a read to the appropriate originating gene. If a strand-specific library was used, Arriba also evaluates the strandedness in ambiguous situations, for example, when none of the supporting reads overlaps a splice-site. + + * breakpoint1 and breakpoint2 : The columns contain the coordinates of the breakpoints in gene1 and gene2, respectively. If an event is not supported by any split reads but only by discordant mates, the coordinates given here are those of the discordant mates which are closest to the true but unknown breakpoint. + + * site1 and site2 : These columns add information about the location of the breakpoints. Possible values are: 5' UTR, 3' UTR, UTR (overlapping with a 5' UTR as well as a 3' UTR), CDS (coding sequence), exon, intron, and intergenic. The keyword exon is used for non-coding genes or for ambiguous situations where the breakpoint overlaps with both a coding exon and a UTR. If the breakpoint coincides with an exon boundary, the additional keyword splice-site is appended. + + * type : Based on the orientation of the supporting reads and the coordinates of breakpoints, the type of event can be inferred. Possible values are: translocation (between different chromosomes), duplication, inversion, and deletion. If genes are fused head-to-head or tail-to-tail, this is indicated as 5'-5' or 3'-3' respectively. Genes fused in such an orientation cannot yield a chimeric protein, since one of the genes is transcribed from the wrong strand. This type of event is equivalent to the truncation of the genes. The following types of events are flagged with an extra keyword, because they are frequent types of false positives and/or it is not clear if they are somatic or germline variants: Deletions with a size in the range of introns (<400kb) are flagged as read-through, because there is a high chance that the fusion arises from read-through transcription rather than an underlying genomic deletion. Intragenic duplications with both breakpoints at splice-sites are flagged as non-canonical-splicing, because the supporting reads might originate from circular RNAs, which are very abundant even in normal tissue, but manifest as duplications in RNA-Seq data. Internal tandem duplications are flagged as ITD. It is not always clear whether the ITDs observable in RNA-Seq data are somatic or germline variants, because ITDs are abundant in the germline and germline variants cannot be filtered effectively due to lack of a normal control. + + * split_reads1 and split_reads2 : The number of supporting split fragments with an anchor in gene1 or gene2, respectively, is given in these columns. The gene to which the longer segment of the split read aligns is defined as the anchor. + + * discordant_mates : This column contains the number of pairs (fragments) of discordant mates (a.k.a. spanning reads or bridge reads) supporting the fusion. + + * coverage1 and coverage2 : These two columns show the coverage near breakpoint1 and breakpoint2, respectively. The coverage is calculated as the number of fragments near the breakpoint on the side of the breakpoint that is retained in the fusion transcript. Note that the coverage calculation counts all fragments (even duplicates), whereas the columns split_reads1, split_reads2, and discordant_mates only count non-discarded reads. Fragments discarded due to being duplicates or other types of artifacts can be found in the column filters. + + * confidence : Each prediction is assigned one of the confidences low, medium, or high. Several characteristics are taken into account, including: the number of supporting reads, the balance of split reads and discordant mates, the distance between the breakpoints, the type of event, whether the breakpoints are intragenic or not, and whether there are other events which corroborate the prediction, e.g. multiple isoforms or balanced translocations. See section Interpretation of results for further advice on judging the credibility of predictions. + + * reading_frame : This column states whether the gene at the 3' end of the fusion is fused in-frame or out-of-frame. The value stop-codon indicates that there is a stop codon prior to the fusion junction, such that the 3' end is not translated, even if the reading frame is preserved across the junction. The prediction of the reading frame builds on the prediction of the peptide sequence. A dot (.) indicates that the peptide sequence cannot be predicted, for example, because the transcript sequence could not be determined or because the breakpoint of the 5' gene does not overlap a coding region. + + * tags : When a user-defined list of tags is provided via the parameter -t, this column is populated with the provided tag whenever a fusion matches the coordinates specified for the respective tag. When multiple tags match, they are separated by a comma. + + * retained_protein_domains : If Arriba is provided with protein domain annotation using the parameter -p, then this column is populated with protein domains retained in the fusion. Multiple protein domains are separated by a comma. Redundant protein domains are only listed once. After every domain the fraction that is retained is stated as a percentage value in parentheses. The protein domains of the 5' and 3' genes are separated by a pipe symbol (|). + + * closest_genomic_breakpoint1 and closest_genomic_breakpoint2 : When a matched whole-genome sequencing sample is available, one can feed structural variant calls obtained therefrom into Arriba (see parameter -d). Arriba then considers this information during fusion calling, which improves the overall accuracy. These two columns contain the coordinates of the genomic breakpoints which are closest to the transcriptomic breakpoints given in the columns breakpoint1 and breakpoint2. The values in parentheses are the distances between transcriptomic and genomic breakpoints. + + * gene_id1 and gene_id2 : These two columns state the identifiers of the fused genes as given in the gene_id attribute in the GTF file. + + * transcript_id1 and transcript_id2 : For both fused genes, Arriba determines the best matching isoform that is transcribed as part of the fusion. The isoform is selected by how well its annotated exons match the splice pattern of the supporting reads of a fusion. + + * direction1 and direction2 : These columns indicate the orientation of the fusion. A value of downstream means that the partner is fused downstream of the breakpoint, i.e. at a coordinate higher than the breakpoint. A value of upstream means the partner is fused at a coordinate lower than the breakpoint. When the prediction of the strands or of the 5' gene fails, this information gives insight into which parts of the fused genes are retained in the fusion. + + * filters : This column lists the filters which removed one or more of the supporting reads. The section Internal algorithm describes all filters in detail. The number of filtered reads is given in parentheses after the name of the filter. The total number of supporting reads can be obtained by summing up the reads given in the columns split_reads1, split_reads2, discordant_mates, and filters. If a filter discarded the event as a whole (all reads), the number of filtered reads is not stated. + + * fusion_transcript : This column contains the fusion transcript sequence. The sequence is assembled from the supporting reads of the most highly expressed transcript. It represents the transcript isoform that is most likely expressed according to the splice patterns of the supporting reads. The column contains a dot (.), when the sequence could not be predicted. This is the case when the strands or the 5' end of the transcript could not be predicted reliably. The breakpoint is represented as a pipe symbol (|). When non-template bases are inserted between the fused genes, these bases are represented as lowercase letters between two pipes. Reference mismatches (SNPs or SNVs) are indicated as lowercase letters, insertions as bases between brackets ([ and ]), deleted bases as one or more dashes (-), introns as three underscores (___), and ambiguous positions, such as positions with diverse reference mismatches, are represented as ?. Missing information due to insufficient coverage is denoted as an ellipsis (...). If the switch -I is used, then an attempt is made to fill missing information with the assembly sequence. A sequence stretch that was taken from the assembly sequence rather than the supporting reads is wrapped in parentheses (( and )). In addition, when -I is used, the sequence is trimmed to the boundaries of the fused transcripts. The coordinate of the fusion breakpoint relative to the start of the transcript can thus easily be inferred by counting the bases from the beginning of the fusion transcript to the breakpoint character (|). In case the full sequence could be constructed from the combined information of supporting reads and assembly sequence, the start of the fusion transcript is marked by a caret sign (^) and the end by a dollar sign ($). If the full sequence could not be constructed, these signs are missing. + + * peptide_sequence : This column contains the fusion peptide sequence. The sequence is translated from the fusion transcript given in the column fusion_transcript and determines the reading frame of the fused genes according to the transcript isoforms given in the columns transcript_id1 and transcript_id2. Translation starts at the start of the assembled fusion transcript or when the start codon is encountered in the 5' gene. Translation ends when either the end of the assembled fusion transcript is reached or when a stop codon is encountered. If the fusion transcript contains an ellipsis (...), the sequence beyond the ellipsis is trimmed before translation, because the reading frame cannot be determined reliably. The column contains a dot (.), when the transcript sequence could not be predicted or when the precise breakpoints are unknown due to lack of split reads or when the fusion transcript does not overlap any coding exons in the 5' gene or when no start codon could be found in the 5' gene or when there is a stop codon prior to the fusion junction (in which case the column reading_frame contains the value stop-codon). The breakpoint is represented as a pipe symbol (|). If a codon spans the breakpoint, the amino acid is placed on the side of the breakpoint where two of the three bases reside. Codons resulting from non-template bases are flanked by two pipes. Amino acids are written as lowercase characters in the following situations: non-silent SNVs/SNPs, insertions, frameshifts, codons spanning the breakpoint, non-coding regions (introns/intergenic regions/UTRs), and non-template bases. Codons which cannot be translated to amino acids, such as those having invalid characters, are represented as ?. + + * read_identifiers : This column contains the names of the supporting reads separated by commas. + + - fusions.discarded.tsv + + The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv. + + +**VISUALIZATION** + +See: https://arriba.readthedocs.io/en/latest/visualization/ + + - fusions.pdf + + A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint. + +.. image:: draw-fusions-example.png + :width: 800 + :height: 467 + + +.. _Arriba: https://arriba.readthedocs.io/en/latest/ +.. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/ +.. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/ +.. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/ +.. _OPTIONS: https://arriba.readthedocs.io/en/latest/command-line-options/ + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jul 27 11:24:44 2022 +0000 @@ -0,0 +1,311 @@ +<macros> + <token name="@TOOL_VERSION@">2.3.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.257246.119</citation> + <yield /> + </citations> + </xml> + <xml name="version_command"> + <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command> + </xml> + <xml name="genome_source" token_assembly_optional="false" > + <conditional name="genome"> + <param name="genome_source" type="select" label="Genome assembly fasta (that was used for STAR alignment)"> + <option value="history">From your history</option> + <option value="cached">Use built-in Genome reference</option> + </param> + <when value="history"> + <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/> + </when> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <validator type="no_options" message="No reference genomes are available" /> + </options> + </param> + </when> + </conditional> + </xml> + <xml name="gtf_source" token_assembly_optional="false" > + <conditional name="genome_gtf"> + <param name="gtf_source" type="select" label="Genome GTF annotation source"> + <option value="history">From your history</option> + <!-- <option value="cached">Use built-in Gtf annotation</option> --> + </param> + <when value="history"> + <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/> + </when> + </conditional> + </xml> + + <token name="@GENOME_SOURCE@"><![CDATA[ +#if str($genome.genome_source) == "history" + #if $genome.assembly + #set $genome_assembly = 'genome.fa' + ln -sf '$genome.assembly' $genome_assembly && + #end if +#elif str($genome.genome_source) == "cached" + #set $genome_assembly = $genome.ref_file.fields.fasta +#end if + ]]></token> + <token name="@GTF_SOURCE@"><![CDATA[ +#if str($genome_gtf.gtf_source) == "history" + #if $genome_gtf.annotation.is_of_type('gtf.gz') + #set $genome_annotation = 'genome.gtf.gz' + #else + #set $genome_annotation = 'genome.gtf' + #end if + ln -sf '$genome_gtf.annotation' $genome_annotation && +#end if + ]]></token> + + <xml name="visualization_options"> + <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> + <section name="options" expanded="false" title="Draw Fusion Options"> + <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/> + <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection"> + <help>By default the transcript isoform with the highest coverage is drawn. + Alternatively, the transcript isoform that is provided in the columns + transcript_id1 and transcript_id2 in the given fusions file can be drawn. + Selecting the isoform with the highest coverage usually produces nicer plots, + in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint. + However, the isoform with the highest coverage may not be the one that is involved in the fusion. + Often, genomic rearrangements lead to non-canonical isoforms being transcribed. + For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2, + which reflect the actual isoforms involved in a fusion. +\ As a third option, the transcripts that are annotated as canonical can be drawn. + Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical. + </help> + <option value="coverage">coverage</option> + <option value="provided">provided</option> + <option value="canonical">canonical</option> + </param> + <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection"> + <help>The fusion of interest is drawn as a solid line in the circos plot. + To give an impression of the overall degree of rearrangement, + all other fusions are drawn as semi-transparent lines in the background. + This option determines which other fusions should be included in the circos plot. + Values specify the minimum confidence a fusion must have to be included. + It usually makes no sense to include low-confidence fusions in circos plots, + because they are abundant and unreliable, and would clutter up the circos plot. + Default: medium + </help> + <option value="none">none - only the fusion of interest is drawn</option> + <option value="low">low</option> + <option value="medium">medium</option> + <option value="high">high</option> + </param> + <param argument="--squishIntrons" type="select" optional="true" label="Squish introns"> + <help>Exons usually make up only a small fraction of a gene. + They may be hard to see in the plot. i + Since introns are in most situations of no interest in the context of gene fusions, + this switch can be used to shrink the size of introns to a fixed, negligible size. + It makes sense to disable this feature, if breakpoints in introns are of importance. + Default: TRUE + </help> + <option value="TRUE">True</option> + <option value="FALSE">False</option> + </param> + <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity"> + <help>This option only applies to intergenic breakpoints. + If it is set to a value greater than 0, then the script draws the genes + which are no more than the given distance away from an intergenic breakpoint. + The keywords closestGene and closestProteinCodingGene instruct the script + to dynamically determine the distance to the next (protein-coding) gene for each breakpoint. + Alternatively, instead of specifying a single distance + that is applied upstream and downstream of both breakpoints alike, + more fine-grained control over the region to be shown is possible by specifying four comma-separated values. + The first two values determine the region to the left and to the right of breakpoint 1; + the third and fourth values determine the region to the left and to the right of breakpoint 2. + Note that this option is incompatible with squishIntrons. + Default: 0 + </help> + <option value="closestGene">closestGene</option> + <option value="closestProteinCodingGene">closestProteinCodingGene</option> + <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$</validator> + </param> + <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By"> + <help>Occasionally, domains are annotated redundantly. + For example, tyrosine kinase domains are frequently annotated as + Protein tyrosine kinase and Protein kinase domain. + In order to simplify the visualization, such domains can be merged into one, + given that they overlap by the given fraction. + The description of the larger domain is used. + Default: 0.9 + </help> + </param> + <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels"> + <help>By default the number of an exon is printed inside each exon, + which is taken from the attribute exon_number of the GTF annotation. + When a gene has many exons, the boxes may be too narrow to contain the labels, + resulting in unreadable exon labels. In these situations, i + it may be better to turn off exon labels. + Default: TRUE + </help> + <option value="TRUE">True</option> + <option value="FALSE">False</option> + </param> + <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect"> + <help>Whether light and shadow should be rendered to give objects a 3D effect. + Default: TRUE + </help> + <option value="TRUE">True</option> + <option value="FALSE">False</option> + </param> + <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors"> + <help>By default, the script colorizes domains according to the colors + specified in the file given in --annotation. + This way, coloring of domains is consistent across all proteins. + But since there are more distinct domains than colors, + this can lead to different domains having the same color. + If this option is set to TRUE, the colors are recomputed for each fusion separately. + This ensures that the colors have the maximum distance for each individual fusion, + but they are no longer consistent across different fusions. + Default: FALSE + </help> + <option value="TRUE">True</option> + <option value="FALSE">False</option> + </param> + <param argument="--color1" type="color" value="" optional="true" label="Color of the 5' end of the fusion."/> + <param argument="--color2" type="color" value="" optional="true" label="Color of the 3' end of the fusion."/> + <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches" + help="Default: 11.692"/> + <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches" + help="Default: 8.267"/> + <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text" + help="Default: 1.0"/> + <param argument="--fontFamily" type="text" value="" optional="true" label="Font to use for all labels in the plots."> + <help>Default: Helvetica + </help> + <option value="serif">serif</option> + <option value="sans">sans</option> + <option value="mono">mono</option> + <option value="AvantGarde">AvantGarde</option> + <option value="Bookman">Bookman</option> + <option value="Courier">Courier</option> + <option value="Helvetica">Helvetica</option> + <option value="Helvetica-Narrow">Helvetica-Narrow</option> + <option value="NewCenturySchoolbook">NewCenturySchoolbook</option> + <option value="Palatino">Palatino</option> + <option value="Times">Times</option> + <option value="URWGothic">URWGothic</option> + <option value="URWBookman">URWBookman</option> + <option value="NimbusMon">NimbusMon</option> + <option value="NimbusSan">NimbusSan</option> + <option value="URWHelvetica">URWHelvetica</option> + <option value="NimbusSanCond">NimbusSanCond</option> + <option value="CenturySch">CenturySch</option> + <option value="URWPalladio">URWPalladio</option> + <option value="NimbusRom">NimbusRom</option> + <option value="URWTimes">URWTimes</option> + <option value="ArialMT">ArialMT</option> + <option value="Japan1">Japan1</option> + <option value="Japan1HeiMin">Japan1HeiMin</option> + <option value="Japan1GothicBBB">Japan1GothicBBB</option> + <option value="Japan1Ryumin">Japan1Ryumin</option> + <option value="Korea1">Korea1</option> + <option value="Korea1deb">Korea1deb</option> + <option value="CNS1">CNS1</option> + <option value="GB1">GB1</option> + </param> + <param argument="--fixedScale" type="integer" value="" min="0" optional="true" label="Apply a fixed scale to all fusions"> + <help>By default, transcripts are scaled automatically to fill the entire page. + This parameter enforces a fixed scale to be applied to all fusions, + which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable. + A common use case is the visualization of a gene that is found to be fused to multiple partners. + By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage + in a single plot one above the other with matching scales. + Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn, + or else dynamic scaling is applied, because display errors would occur otherwise. + The default value is 0, which means that no fixed scale should be used + and that the scale should be adapted dynamically for each fusion. Default: 0 + </help> + </param> + <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot"> + <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes. + The plots can be cropped at a fixed level by passing a non-zero value to this parameter. + When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level. + When two comma-separated values are given, the cutoffs can be specified independently for the two plots. + A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage) + and that the coverage plots of both genes should be on the same scale. This is the default behavior. + A value of 0,0 also indicates that no cropping should be applied, + but the coverage plots of the two genes have different scales: + each one is scaled individually to the peak coverage of the respective gene. + Default: 0 + </help> + <validator type="regex" message="">^\d+(,\d+)?$</validator> + </param> + </section> + </xml> + <token name="@DRAW_FUSIONS@"> +draw_fusions.R + --fusions='$fusions' + --alignments='Aligned.sortedByCoord.out.bam' + --annotation='$genome_gtf.annotation' + --output=fusions.pdf + #if $visualization.cytobands + --cytobands='$visualization.cytobands' + #end if + #if $protein_domains + --proteinDomains='$protein_domains' + #end if + ## Visualization Options + #if $visualization.options.transcriptSelection + --transcriptSelection=$visualization.options.transcriptSelection + #end if + #if $visualization.options.minConfidenceForCircosPlot + --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot + #end if + #if $visualization.options.squishIntrons + --squishIntrons=$visualization.options.squishIntrons + #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity + --showIntergenicVicinity='$visualization.options.showIntergenicVicinity' + #end if + #end if + #if $visualization.options.mergeDomainsOverlappingBy + --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy + #end if + #if $visualization.options.sampleName + --sampleName='$visualization.options.sampleName' + #end if + #if $visualization.options.printExonLabels + --printExonLabels=$visualization.options.printExonLabels + #end if + #if $visualization.options.coverageRange + --coverageRange='$visualization.options.coverageRange' + #end if + #if $visualization.options.render3dEffect + --render3dEffect=$visualization.options.render3dEffect + #end if + #if $visualization.options.optimizeDomainColors + --optimizeDomainColors=$visualization.options.optimizeDomainColors + #end if + #if $visualization.options.color1 + --color1='$visualization.options.color1' + #end if + #if $visualization.options.color2 + --color2='$visualization.options.color2' + #end if + #if str($visualization.options.pdfWidth) + --pdfWidth=$visualization.options.pdfWidth + #end if + #if str($visualization.options.pdfHeight) + --pdfHeight=$visualization.options.pdfHeight + #end if + # fontFamily + #if $visualization.options.fontFamily + --fontFamily=$visualization.options.fontFamily + #end if + #if str($visualization.options.fontSize) + --fontSize=$visualization.options.fontSize + #end if +</token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Aligned.out.sam Wed Jul 27 11:24:44 2022 +0000 @@ -0,0 +1,89 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:22 LN:269079 +@SQ SN:9 LN:515509 +@PG ID:STAR PN:STAR VN:2.7.8a CL:STAR --runThreadN 12 --genomeDir tempstargenomedir --genomeLoad NoSharedMemory --readFilesIn /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368710.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368711.dat --readFilesCommand zcat --limitBAMsortRAM 122880000000 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM ch --outSAMunmapped Within --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outBAMsortingThreadN 12 --outBAMsortingBinsN 50 --outSAMattrIHstart 1 --winAnchorMultimapNmax 50 --chimSegmentMin 12 --chimOutType WithinBAM Junctions --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan Singleend --twopassMode Basic +@CO user command line: STAR --runThreadN 12 --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --readFilesIn /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368710.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368711.dat --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM ch --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outSAMunmapped Within --chimSegmentMin 12 --outBAMsortingThreadN 12 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 122880000000 --chimOutType WithinBAM Junctions --chimOutJunctionFormat 1 +BCR-ABL1-46 163 22 225687 60 71M2994N7M1344N72M = 225737 5255 AACTGGAGGCAGTGCCCAACATCCCCCTGGTGCCCGATGAGGAGCTGGACGCTTTGAACATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTG CCCGGGGGG=GGGJJJGGJJJGGJJJJCJJGGJJGCJGCGGGC8J8JGGJJJJJGJJC(JGCCG=GGJJGCCCGC8GCCGGGGGG=GGCGGG1GG=GC1G=CJCJJCCCGGCGG1CGG1GGGGGGGG=GGGGGCCGCGGG8GGGCGG=GG NH:i:1 HI:i:1 AS:i:285 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-72 163 22 225696 60 62M2994N7M1344N81M = 228752 5264 CAGTGCCCAACATCCCCCTGGTGCCCGATGAGGAGCTGCACGCTTTGAAGATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCA CCCCGGGGGGGGGGJGJCCCJ1GJJJJGCGGGCJJJ=C1JJGGJGG8JGC=CCGJ1JGG8GGGGGJCGJCCGGGCG=CGGGGGGCGG=GGCGGG=8CCGCGGJJJ=JGGGCGGGGGCCGCCGGGGGGGGC=CCGCG8GGGGGC1GGGGCC NH:i:1 HI:i:1 AS:i:290 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-46 83 22 225737 60 21M2994N7M1344N105M717N17M = 225687 -5255 GCTTTGAAGATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGG =GGCGGGGGGG=GGGCCCGCCCGGGGGGGGGGCCGGGGCGG8CGCGGG1JGGCCGG(C=GCCCGGGGGGCGGGGGCGCGGCGGJCGGGJJGJGGGJJCGGGJJJGJJJJJJJGJJJJGGGJJJJJGGJJJJJGCJJJCGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:285 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-72 83 22 228752 60 3S7M1344N105M717N35M = 225696 -5264 TCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAAT =GGGGGG==GGGGCCCC=GGGGG=GGGGCGGGCGGGGGGG=CGGCCGCCJGGCGGGGG=GGG8GGGCGGC=G=CCJGGGGGGCGJJGJJCGGGGGGJJJGCJCCGJG=JJJGJGJJCJJJJGJJJJJJJ=GCJGJGCGGG=GGGGGGCC= NH:i:1 HI:i:1 AS:i:290 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-4 99 22 230111 60 97M717N53M = 230176 889 AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCC C==GGGGGGGGGGJJJJ1JJJGGJJGGJGGJJGJJCJGJGJJCGGCJGCJJJJCGJGGGGJGGGGGGCCGG8JGGCGCGG=GGGGGGGGGGGGGG=GCCGJGGGCCGGGGGG1GGGGGGCGCGGCGGGGGG=GGGGGGGGGCCGCGGGCC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 XS:A:+ NM:i:0 +BCR-ABL1-18 99 22 230118 60 90M717N60M = 230165 882 CCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGTAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCAATCAGCCACTGGAT CCCGGGCGGGCGGJGJJJJJJJJJ=GCJJCJJJJJGJJJGJJGJJJCGGJJGGJCGJC=GG8GCGJGCGCG==GGGCGGGGG1CCCGCGGGGGCGGCCGGC=GCGGG=GGGGCGGGGCGCGGGGGGG=GGGCGGGG(GGGCGGGCGCCGG NH:i:1 HI:i:1 AS:i:266 nM:i:2 XS:A:+ NM:i:2 +BCR-ABL1-12 163 22 230132 60 76M717N74M = 230923 868 GAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCA CCCGGGGGGGGGGJGGJJJJJCCJJCJJGJJGJJGGCJJJCJCGGGJJ=CGJGJJJJGGCGGGJJJ==GG(GGC=GGGGGGCGCGG(GGGGC1C8GCC=GG=C=CCJGGGGGG8CGGCCCGCGGGGGGGGCGGGG=GGGGGCGGGG=GGC NH:i:1 HI:i:1 AS:i:227 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-18 147 22 230165 60 43M717N75M32S = 230118 -882 CTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTT =GCGGGGG(GGGGGGGGGGGCC=GGC=GGCGGCCGGGGCGGG8JJJJ=GCGGGGG1GGGCCGGGCCGGGCGGCGGGJGC8GCCGCGGCG=GJCGJJGC8GC1JGG=GJJCJC1JGJGGJJJGJGCJJJ=1JJJJ=JGGCG=GGCGGGCCC NH:i:1 HI:i:1 AS:i:266 nM:i:2 XS:A:+ NM:i:0 +BCR-ABL1-4 147 22 230176 60 32M717N75M43S = 230111 -889 CCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGG CGGCGGGGGCGGCGCCG=GCGCGGGG8GCG881CGG=C=GCCGJJCJCCCGGG8GGCGG=GGGCCCGGCGGCCCCGGCGGGG=GGCGCJJGCGGJG1JGJJJ8JGJJCJJJ(JJGJGJJJGGJJGJCC1JJCGGJGG=GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 XS:A:+ NM:i:0 SA:Z:9,275100,-,107H43M,60,0; +BCR-ABL1-12 83 22 230923 60 19S77M54S = 230132 -868 CGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAG 8CCCGGCCGGCCGGGGGCGG1CCG=GGCGGGGGC1GGGGCCGCGGGGCCJGG=CGGCGGGGCGCGCGGGCGGCGGJG==GGCGCJGCGGGCJGGGGGGGCJGJGGJJJGJGGGGCJJJGJJJGGJGJJJGJJCCJJGGG1GGGGGGG=CC NH:i:1 HI:i:1 AS:i:227 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-60 2145 22 230961 60 39M111H 9 275110 0 TCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA =CCGGCGGGGG=GJJGJGGGCJJCJJGJCGJG(J(JJJG NH:i:1 HI:i:1 AS:i:38 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,39S111M,60,0; +BCR-ABL1-76 2145 22 230973 60 27M123H 9 275139 0 CAGCCACTGGATTTAAGCAGAGTTCAA CCCGGGGCGGGCGJJJJJGJJJGJJJJ NH:i:1 HI:i:1 AS:i:26 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,27S123M,60,0; +BCR-ABL1-28 2209 22 230978 60 22M128H 9 275128 0 ACTGGATTTAAGCAGAGTTCAA CCCGCGGGGGGGGGJ=GJCGJJ NH:i:1 HI:i:1 AS:i:21 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,22S128M,60,1; +BCR-ABL1-64 99 9 275097 60 6S144M = 275140 756 AGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGG CCCGGGGGCGGGGGJJJGJJJGGJJJJJCJJJJGGJJJGJJGJGJG=GGJG=JJJJCGCCC==JGGCGGGCJG1CCCCGG8CGGGGGGGGCCGC=CGCGGJGGGGCGCGGGGGGGGCCGCGGGG=GCGGGGGGG=GGGGCGGGGGGCCGG NH:i:1 HI:i:1 AS:i:290 nM:i:2 XS:A:+ NM:i:1 +BCR-ABL1-54 99 9 275097 60 61S89M = 275097 140 CCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTGAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTC CCCGGGGGGGGGGGJJJJJGJ=JJJJJJGJJJGGJJJJJJJCJJG8JJJGJJGJ=GG=JJJGGCGGCGGJGC(GGGGGCGC8CGGCGCCGGC=GGGCGGGJG1GGGGGG1CG=GGGGC=1G1CGGGGGCCGGGGCGG=CC=C=CGGGGG8 NH:i:1 HI:i:1 AS:i:219 nM:i:4 NM:i:2 +BCR-ABL1-54 147 9 275097 60 10S140M = 275097 -140 AAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACGTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTT =GGGGGGGCCCCGCCGGG=G(GGGG=CGCGGCGCCGG=GGGGGCJJJ=GC8C1GGGGGCG8GCCGC=GGG1GCCGGJC8GCGGCGCGJGJJJG1CGJGG=CJJJGGGGJG=CJGJJJJCJCJJGGJJJJJGGJGGJJCGGGGGGGGG=CC NH:i:1 HI:i:1 AS:i:219 nM:i:4 NM:i:2 +BCR-ABL1-48 163 9 275097 60 3S147M = 275137 753 GTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCA CCCGGGCGGGGGGGJ1JJJJJJJCJJJCGJJCGGJCJJGJGGJJJGGGCGJJ=GJJJG=JCG=GJGGGC8=GCG=G=GCCGGG1CG1GC=GGG8GGGGG1GCJJCJJCCGGCGCCG=CGCGGGCGG=GCGGG1CGC1CGC=CGGGCGGGG NH:i:1 HI:i:1 AS:i:295 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-2 99 9 275097 60 62S88M = 275097 134 TCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCCTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCT CCCGGGGGGGGGGGJ1JJJJJJ=JGGGGJJJCGCJJJCJJJJGGCJGGGJCJGGJJGJCGJGG1GCG=CGG(G=CGGG1GGCCGGGGGGGCGGGG=GCCGJGGCGCGGGGCCCG1GGGCCGGG8GGCGGCGG=CC(G=GC1GGCCGGGCG NH:i:1 HI:i:1 AS:i:214 nM:i:3 NM:i:2 +BCR-ABL1-2 147 9 275097 60 16S134M = 275097 -134 GGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTAT CGGGC=GGGGG=GGGGGGCCCCG=GG8=8CCGCGGGGGCGCGCJJCJ=CCCCC81GGGGC=GGGC8C8GGCGCGJCCGG8JCCGCC1GGCGGCJGGGJJJGGJJJJJCGGJGCJJJJJJG=JGJGJJJJGJJJGGJGCGCGGGGGGGCCC NH:i:1 HI:i:1 AS:i:214 nM:i:3 NM:i:1 +BCR-ABL1-76 99 9 275100 60 27S123M = 275139 752 CAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTG CCCGGGGCGGGCGJJJJJGJJJGJJJJJJJJJGJ1JCJJGJGGJJJGJJGGJJJ8GGJJGGGJJ=GGCGGGGGG=GGCCGGG8GC=GGGG=GCGGCGGGGJGG=GGGG=GGGGGGGGCGGGGCCGGGCG=GG(G=GCGCCG1CCGGCGGG NH:i:1 HI:i:1 AS:i:273 nM:i:0 ch:A:1 XS:A:+ NM:i:0 SA:Z:22,230973,+,27M123H,60,0; +BCR-ABL1-68 99 9 275100 60 1S149M = 275125 175 AAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGA CC1=GC=GGGGGGJJJJGJJJJJGGJJJJJJJGJJJJJ=(GJGGG8CCGJJ=GJGGGGJGJGJ=GGGCCGCGGCG1CGCGGGGGGGCGCCGCGGCGGGGGJGCC8GCGGGGCGGC=GGGGG=GGGCCC=GCGGGGGGCGCGGGCGGCGCG NH:i:1 HI:i:1 AS:i:291 nM:i:3 NM:i:0 +BCR-ABL1-60 99 9 275100 60 39S111M = 275110 160 TCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCA =CCGGCGGGGG=GJJGJGGGCJJCJJGJCGJG(J(JJJGGCGGGJJJGCJGGG1G=JGGJJGCJCCGGJ(JJCCGCC=GCGGGCGGGGG1GGGGCGCGG(JCGCGGGGGGGGGGGGCCGGCGCGCGGGGGGGCGGGGCGG1GGGGGGCGC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 NM:i:0 SA:Z:22,230961,+,39M111H,60,0; +BCR-ABL1-28 163 9 275100 60 22S128M = 275128 741 ACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCCCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTG CCCGCGGGGGGGGGJ=GJCGJJJ1JCJJJJGJJJJJCCJJJJG8JJCC=CGGCGGJGGC(JGGG=GCCGCGCJ8CGGG=GGGCGGGGGCGGCCGGCCGGGCCJ=JC=CGCGCGC1G8GCCGGGGGC=GCGGGCGGGGGGGGGGGGGCGCC NH:i:1 HI:i:1 AS:i:274 nM:i:2 ch:A:1 XS:A:+ NM:i:1 SA:Z:22,230978,+,22M128H,60,0; +BCR-ABL1-4 2193 9 275100 60 107H43M 22 230111 0 AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGG CJJJ(JJGJGJJJGGJJGJCC1JJCGGJGG=GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:42 nM:i:0 ch:A:1 NM:i:0 SA:Z:22,230176,-,32M717N75M43S,60,0; +BCR-ABL1-60 147 9 275110 60 150M = 275100 -160 GCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCT GCGGCCCGCGG=GG8GGCGGGGCCGCC=GCGCGGCG1GGCGG1JCJJ8CCCG=GGGGGGCG=GCGGGG18CCGCG=GGGG1CGG8C=GGGGCGGCJGJGJGJGJJGGJGJJJGJGJJJGGJC(JJJGJJJGJCJJGCGGGGGCGGGGCC= NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 NM:i:0 +BCR-ABL1-68 147 9 275125 60 150M = 275100 -175 TGACTTTGAGCCTCAGGGTCTAAGTGAAGCCGCTCGTAGGAACTCCAAGGAAAACCTTCTCGGTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGG G=CGGCGGGCCGCGCGGCCGG8GCCGCC(GGC=8=GGG=GGGCJ1=JJCCGGGCGGGGGGGG=GCGGGGCGCG==GGCGGGGGJGCCJJGGCCG=GCCCGGJCGGJJJJJ=GJJJJGJCJ=GCJGJGJJJC1GGJJJGGG=GG1GGGCCC NH:i:1 HI:i:1 AS:i:291 nM:i:3 NM:i:3 +BCR-ABL1-50 99 9 275125 60 150M = 275169 757 TGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGG CC1GGCGCGGGG=JGCJJJJJGJJJGJJGGJJGJJ8JGCGJJJJJJ8CJJGJJCGJGGGGJJCCG=CGGGGGCCCG=CGGCCGCGGGGGCGG=GGGGGGGCCGGG==GGGGGCCGG=GGGGCCG=GGGGGCCC=GGCGGGGCCGGCCGGG NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-28 83 9 275128 60 146M563N4M = 275100 -741 CTTTGAGCCTCAAGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGA GGGGGCGGGG=C1=8GGCGCGGGCGCGGGGG=GC=GGGGCG1CCCGCGGCCGGGC=GG=GGGGGCCGGGGCGGGCGJJGGGGCGGJ1JGGGGCGGJGJGGJJJCGGCJJCGJ=GJGCGGJJJJGGJJG1JJJGG1JJ=GGCGCGGG1CCC NH:i:1 HI:i:1 AS:i:274 nM:i:2 ch:A:1 XS:A:+ NM:i:1 +BCR-ABL1-48 83 9 275137 60 137M563N13M = 275097 -753 TCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCG GGGCGGCGCGGGG8GGGGGCGGCGGGCG1GCGCGG8GCGGCGC1G8CCGCGCGGCCGGGGGCGCCGCC1=CCCCGCCJCGGGGGGJJGJC=CCJ8JJC=JJCGCJJJGJJJJJJJJJJGJJGGGCJJJJJJJGJGJGCGGCGGGCGC=C1 NH:i:1 HI:i:1 AS:i:295 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-76 147 9 275139 60 135M563N15M = 275100 -752 AGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGG CGGCGGGGCGGGGGGCGCCGCGCGGGGC=GGCGCCGCGCGGGCJJCJC1GGGGG=GCGGGGG=GGGGGGGGGGGGGCGGCGGGGGGJGJCGJGGJGJCJGJJJJJG8JJCJGG1JJJJJJJG8(JJJJJGJJJGJJJGGGGGGGG1GCCC NH:i:1 HI:i:1 AS:i:273 nM:i:0 ch:A:1 XS:A:+ NM:i:0 +BCR-ABL1-64 147 9 275140 60 134M563N16M = 275097 -756 GGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTGTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGT C=GGGGGCGGCGGGGGGC=GGGGC1CG=1=GGGCCC=GGGCGCCCCJJGCGCGGGGCGGCGCGCCGCCGCGGGGGCGC1GGGGG=GG1CGJGJJJ(CCGGJJGCGJGJGJJJGGGCGJGJJJJJJJJJGJGJGJJJCGCGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:290 nM:i:2 XS:A:+ NM:i:1 +BCR-ABL1-14 99 9 275146 60 128M563N22M = 275170 737 GAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGG CC=GGGGGGGGGGJGJJCJGJJJGG1JJGJ=JGGGJJJJGGJJJGCJJCGJJGC=GCJGGJGGCGGGCCGGGCGGCGCGGGGGGGGGGGGCC8GGGGCGCJCGGGCCCGCG8GGGGCGGGCGGCGGGGGGCGGGGGCGGG=GGGGGGCCG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-78 99 9 275151 60 123M563N27M = 275200 762 AAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATA CC=1G=GGGGCGGJJJJGJJGG8JJCJGJGJJ8JJJJGJCGJGJJ=JGGGCGJCJCGGG=JJJJGGG=JGC=GGGCGGGGGGCGGCG=GCCGGGGGGCGGJCGCCGCGGGGGGGCCGGGGCGCCGGG=GGGCGCGGGGCGGGCCGGGGGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-62 163 9 275157 60 117M563N33M = 275215 771 CTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACA CCCCGGGGGGGGCJGGGJJGJJJJJJJ=GJJCJJGJCJGJCGCGCGGGCCJGJCGJ81JC1GGGGGCG8GGCGGGGCG1C1GGGGCGGCGCCCGGG=GC=CGCJJJJGGGGGCGGCGC=8GCCGGGGGGGG=GCG=1GGGCGGGCGG1CG NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-50 147 9 275169 60 105M563N45M = 275125 -757 CCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGT CCGCCCGGGGGCGGGG1GCGGGGGGC8CGG=CGGCCC=CGGGCCJ(JJ=GGCGCGGGGCGGGGGCC8GCCCGGCGCGGGJ8GGGGCC1JJGJCGGJJJGJG8JJGJJJJCJJJGGJGGGCJGGJJJJGGGJJJ=CJCGG=GCGGGGG=CC NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-14 147 9 275170 60 104M563N46M = 275146 -737 CAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTG 1CGGGGGCGGCCGG1CG=GGGGGGGCGGGGGCCGGG1CGCGCCJJJJJCG1CGGGCCGCGGGGGGGGGGGGCGGGGGGGCCGGGCGJJGG=JJ(J18GJCJGJ8JJGGJ=JJGJJGGGJJJ=JJJJCJJJJJJJJJGGGGGGG1GGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-20 163 9 275172 60 102M563N48M = 275219 760 AGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTG CC=GGGGGGGGGGJJGJJJJJJCJJ=JJJJGGGGJCJJGCGCGJGGCCCJJJGJJJJCGGJG=GGJGGGGGJGJGCCGGGGCCG=GG=C=G=GGCCGGGCGCCCC=JG11GGCCGCCCGCGCC8CGGGGCC1CGCGGG=GG=CCC1GGCG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-26 163 9 275174 60 100M563N50M = 275216 755 GAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGCAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAA C1CGGGCGGGGGGJJJ=JJGGCGGGJJGJJGGJGGJJGJCJGJJ=GGCJJGJJGGCGCGCGGG=JGGG8GGGGCGGGGGCGCCCGGGCGGGCCCCCG=GGGCJ(JCJ=GGCCGGGGGGGGGGGGGCCGCGGGCCGGGGGCGCGGGGGGGG NH:i:1 HI:i:1 AS:i:298 nM:i:2 XS:A:+ NM:i:1 +BCR-ABL1-34 99 9 275183 60 91M563N59M = 275223 753 CTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCCCTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACC CCCGGGGGGGGGGJJJJJGJGJJGG=JJJJJJGJJJGJGJC1JGGGJGGJJGGGJJGG=GCGJGGJCGGGGGGCG=GGCGG1CGGGG=CGGCCGGGCGGGJ88=CGCG=GGGGGC=GGCGGGGG1GGCCGGGG1GGGCGGGGCCCGCGGC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-80 99 9 275199 60 75M563N75M = 275250 764 AAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAACTGGCCAAGGCT CC=GGGGGGGGGGJJJJCJCJJJJJJGGGJJJCJGCCJJJJJ=JCGJJJ=J8JGJGJ=J=JGG=CJCCGG1GG=CGGG=8GG=GCGCCGGCGCGGGG8GGJG1CGCGCCGCCGCGG=GGGGCGCGGGGGG=G==GGCC(GGCGGGGCGCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-8 163 9 275199 60 75M563N75M = 275246 760 AAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCT =C=GG(1GGGGGGJGGJGCCJJCJJJJJJ=GJGGJJGJ=JJGCGCGJJJJJGGJ1GGJJG8C8GGG=GCCG8GGGG1=CGG88CG=GG8GG=GGGCGG8GGCJ18CJ=CGGCGGGG1CC=GCCGCGGG=GGGCGGCGCC8GCCGCGCCGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-78 147 9 275200 60 74M563N76M = 275151 -762 AAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTG GGGGGCG8GGGGGGGCCGCGG=GCCGCGCGCGGGGGGGC=GCGJ88JJ=CGCGGGG=CGGGGG(GG=G(CCGCGGCJGJGGGCCGGCCJJGGJJJGJJGG1G(JJJGCGJJG=J=GJJJGJJJJJ=CGJJJGJGGJJGGCGGCGGGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-42 163 9 275204 60 70M563N80M = 275245 754 GACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTC CC=GGGGGGGGGGGGJJJGGJJJ=JJJGGGJJGJGCJJJJ(GJGJJCCJGGGJCGJGGJJJGG=G1C8GCGGGG18GCC=GGGGGCCCGC1GGGGCGGCGG=CCJCCGGG==GGGGGGGG1G(GGG=C=GGGG88=CC=GGCGGGGCGGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-62 83 9 275215 60 59M563N91M = 275157 -771 TTTCGTTGCACTGTATGATTTTGTGGCCGGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTA GCCC1CCCCCGCGCCC=GGGGGGCCGGC8CGGC1GGC=CGGGGCCCGGC8GCC=GCGGGCGGGGGGGCCGJGGGGGGGGGJGG=GJGCGJGGJ=JJGJGJCG=JJJJGJJJJGJJJGJJGCGJCJ=JJJJJGJGGJJGGGGCGGGGGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-26 83 9 275216 60 58M563N92M = 275174 -755 TTCGTTGTACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTAC CGGGGGC(GGGCGGCGCCGGGCGGCGCCGGGCGCGGGGCGGC==GGCCG=1GCCGGCGGCGGGCCCGGG=GGGCGCCCCJJGCCC1GJJCJGGGJJJG8JGG=GJJ=GGJJJJCJGCCGJJJJJJGJJJJJGGJGJJGGGGGGGCGCCCC NH:i:1 HI:i:1 AS:i:298 nM:i:2 XS:A:+ NM:i:1 +BCR-ABL1-44 163 9 275217 60 57M563N93M = 275260 756 TCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACA C=CGGGGGGCGGGJJJJJGJGJJJJJ1JJJJJJ1JJJGCGGG=JGJGJGGJGGCGGCGJGCJG=JJGGCJCGCCCGGGGCCCGGGC=GG=CGGGGGGGGGGGCJJJJGC=GGGGCGGCGGC=CCGG8GGGCGCGGCCCGGCG=GGCGGGC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-40 99 9 275219 60 55M563N94M1S = 275838 769 GTTGCACTGTATGATTTTGTGGCCCGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATG CCCCGGGGGGCGGJJJJGGJCJJJ(GJJ=JJJJJCJJJGGGGJJJGGGJJCJJJGJCJCCJJ(CJ=CGGGJ=GGGCJCGGGGCGGGCGGGGGCGGCGGGGCCGGCGCCGGGGGGCCGCGGGGGGGG=GGGCGG=GGGGGCGGG8G=CGG1 NH:i:1 HI:i:1 AS:i:297 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-20 83 9 275219 60 55M563N95M = 275172 -760 GTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATC GCG=GGGCC8GCCGCGGGGGGG=GGCCGGCGGGGCCGGGCGG8CGGCGGJGCGGCGGGGGGCGG=GGG1GCGGGGGGGGGC==JJGG=GGGCCJGGGGGGJJJJJGCCGJJGGJGJCJJCJJJJJGGJJJJGJJJJ1GGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-34 147 9 275223 60 51M563N99M = 275183 -753 CACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGC CGGG8GCC=GGGCGGGGGGCGGGGG=GGGGGGGCGGCGCGGGGJJJJCCCGC1GGGGG8GGCC=GGGGGGGGGGGCCGGCCCG=GCJJJGGGGGG81J8=CGJGGGGJGJJCJGGJGGJGCCJJGJJJJJCJJJJGJGGGCGGGG=GCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-22 99 9 275237 60 37M563N113M = 275864 777 GTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTG CC1GGGGGCGGGGGGCJJGCGJCJJJJJJJJGJJJJGJJGGG1JGCJJCJJGJJJJJGGGGJGJJCGJJGCC8CGGCGCGGCGCCG1GGCCCCGC=GG=GJCGGGGCGCG=GGGGGCGGC=CGGGGGGGGGCGGCCCGGG(G8GGGGGGG NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-42 83 9 275245 60 29M563N121M = 275204 -754 TGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACA GGGCGGGCGCCGGGGGCGGGGGG=CGGGGC1CGCGGGCG=GGCG=GGCCCGGGGCGCGGCGGCCGGGGGGG(GG=GGG=GGGCCGGJJGJJ=GGGGGJJGCGJGGJJJJJJGCJGJGG(GGJJJGJJJJJJJ8GJJJCGGGGCGG1G1CC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-8 83 9 275246 60 28M563N122M = 275199 -760 GGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACAC G=GGCGGGGG=GGGGGGGCCGCCGCGCGGCCGGCGGGCCGGCGGCGGGGJGG=GGGGGGGC=GCGGGCCCG=JGCG=GGGJGGGJGJGGGJCGCGCGGJGGJJJJJJGJGJGJJJG1JJJJJJJJGJCGGJJJJJJCGGGGGGGGCGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-80 147 9 275250 60 24M563N126M = 275199 -764 ATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCT CCCCCGGCC8GCG=CGCGCGGG(GGGGGGGGC=GGG=GG=CGCJJJJJGGGGC==G8CGGG=GCGGC1GGGC(GG=G=GGCGJC8GCGJGJCGCJGJGCGJGJJJGGJJGJGJCJJJJGJGJJJGGJJJJJJGJJJJ8GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-30 163 9 275254 60 20M563N130M = 275867 763 CACTCTAAGCATAACTAAAGGTGAAAAGCACCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTA CCCGG1GGGGGGGJGJCJGJGJJJ(JGJJ(JGJGC=GJJJGJJGGJGGJJJJGGJGGCCCCJG8CG=GCJCGGGJ=GCGJ1CGGGGCCGCG8CG=GGCGGC(CJJC=CGGCGG(CGGGGGGCGCCGG=GC1GCGG=G1CGGCCCCG===8 NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-52 99 9 275256 60 18M563N132M = 275877 771 CTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCCTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACC CCCGGGGGGGGGGGJJGCGJGG8GJJJGJJGJG=G=JJGGCJGGGGGJGGJJGJJGJGGGCJ=GJGGGCGJCGGGGGGG8CGGGGGGC=GGCGGGGCGCGJCGCGCCCCGCG11GGGGGGGGGGGGGGCCCGGGGCCGGCGGGGGCGGCG NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-44 83 9 275260 60 14M563N136M = 275217 -756 AAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGG CGGGCGCGGGGCGCGGGGGCGGGGGGGGGCGGGGGGGG=G1GGGCGCGGCGCGGGGGGGCGGCGCCGCGGC==GGG=1GGG=CJJGCGJGJJJCGCJJ8GJJGGGJJGGJJJGJJGJJJGJJJJJJCJGJ=GGJJ=JGGGGGCGGCGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-40 147 9 275838 60 150M = 275219 -769 TGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAA =GCCGGGGCGGGG=GG1G8G=G(GGCGGGGGGGGC1C=GCGG=J8JJ1GGGGGGGGGGGGGGGGGC=1G8CGGCJ8GC1GGCGCCGJG1GGJGGJGJ8JJCJJJGJ8GGJJJ=JGJJG=CGG=JJJJJJJ8JJ=JJGGGGGGGGGCGC=C NH:i:1 HI:i:1 AS:i:297 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-16 163 9 275840 60 150M = 275888 198 AAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCACCAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATG CC8GGG1CCGGGCCJJGJG(JJJJJ(JGJCJGJJJJJJJJGGJGJGJJCCJJJGJGGGGCGGG=C=JGJJG=C8GGGCGGGGGC(GGCGCGCGGCG(CGG=1(C=JCGGGCCGGGGGCGCGGGCGGCGGGCGGCCGGGGGGGG8GGGCGC NH:i:1 HI:i:1 AS:i:296 nM:i:1 NM:i:1 +BCR-ABL1-6 99 9 275846 60 150M = 275903 207 TCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTG CCCGGGGGGCGGGGJJGJGJ=JJJJJJJJJJGJGGJJJGGJC=GGGGJ=GGCJJJGCGJGJGJJGJGCGJGGJGJCGCGGGGGGGGGG8GC8GC8G=GGGJ=GCGGGGGCCGCCGGGGGGGG1G1=GCGC81CGGGGGCCCGGGGGCGGG NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-32 99 9 275850 60 150M = 275894 194 GGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTA CCCGGGGGGGGGGJJGGJJJ=JJGJ8JGJ=JGJG=GGGJGCCJJJC=J8JJ=GCCJC8JC=GGGJGG(GGCJGGGG1GC=GJ=GCCGGCCGGG=GGGGGGJGCGGCGG=CGGCGCG=GGC=CGGGGCCGGGGGGCCCCGCCGGGCCGGGG NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-38 163 9 275854 60 150M = 275900 196 TTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTG CCCGCGGGGGGGG=GGJGJGJJJ1=GGCJJJCGJ=GJJJGGCJGGCGJGGJJCGJCGJGGG=GGGGJCGGGGGGJGGGGGGGGG8C=G=GCGG==CG8GCG=JCJJCCGG8CGGCGGCCGGGCCGCGGCGGG=GCGGCGG=8CGGCGCG= NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-22 147 9 275864 60 150M = 275237 -777 ATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCG GGG1C8GGG=C=GGGCGCGG=GG=GCGGGGCGGGCGCGGGCGGJ1CCJCCC8GCC=GGCGGGGGGGCGCGCGGGCCGJGCGJGJGGJGCJGGGGGCGGGJ(JCGGGJJJJJJG=1GGJJJGJJJGGJJJJJJGJ1JJGG=GGGGGCGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-30 83 9 275867 60 150M = 275254 -763 ACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGA CG8GC==GCGCCGGGGGGG8=CGGGGGC=CGGCGGGGGCG=GGGC=GCCJGGGGCGGCGCGGGGCGCGGGCCCGJGGG8(8GC8GCGCGCJGGGGGGJGGGJGJJJJJGJJJJCGGJJGJJJ=JJJJGGJ=JJJJGGGGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-36 99 9 275872 60 150M = 275919 197 GGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAAT CCCGGGGGGGGGGJJJGGJJ=JJJJGJJJJJ=GGJJJCJ=JGGGJGGJGJJGGGGCGCG=JGCCGJGCJGCGGGJGGCGCG1GJGC=8GGCCCCGG8CCGJCCGGGCGGGCGGGGGCG1GCCGGCGGGGGCCCGGCCCG(G8GC8=CCGC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-70 163 9 275874 60 150M = 275911 187 GGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGG CCCGGG==GGGGGJJJJJJJJJJJ=GJ8J=GJGJGJGGJCCJJJCGG1=GJGJG18JG=GGGC1GGGJ8GCCC1=CCGCGGG(GC1GCG1GCCGC8GG1GG=JJCJ1GGCGCCGCG(CGGCGGGGGG(GGGGGGCGCCGGGGCGCGCCG= NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-52 147 9 275877 60 150M = 275256 -771 ATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAG CG=GGGGC(CGGGGGGGCCGCGCCGGGGG=GGCC8CGGCCCCCCJ=CJ=GGGGGGGGCG=GGGGCG(GC1GGGC=GJCCCGJ=88GJGGJGJGCJGGJJGGJJJGJJJJGCGJJGGJ(GJGGJCJJJCJJJJJ=(JJGGGGGGGGGCCCC NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-56 99 9 275885 60 150M = 275928 193 AAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGG =CCGC=GGGGGG1JJJGJGJJJCJJCGJJJJJJJJJJCGJJJJJJGGCCJ1JGCGGCGJ8GG(CJGJGJCGGCGG1CC=CG=GCC=GGGGG=GGCGCCG1CGGGGGGG1GGGGGCGGGCGCGGCGG811G8CCGGGGCGGGGGCCG=CGC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-16 83 9 275888 60 150M = 275840 -198 CCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGC CGGGGGG=GGCGGGCGGGGGGGCGGGGCGGGGCCCG=CGGGGGCGGGCCCGG8GCCCGG8GCGGC=GCCCGGGGGGCGGGCGGJGGGCCGGJCGGJJGJGGGGGJJJJGJJGGJJGG=JGGJJGGJ=JGJJJJJJGJC1GGGG=GGG1C1 NH:i:1 HI:i:1 AS:i:296 nM:i:1 NM:i:0 +BCR-ABL1-32 147 9 275894 60 150M = 275850 -194 CCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGA 8GCCCCGGCGCGC1GGGGCGGCCGGGGCG1(GG=GG=GCGGCGJCJJCGG8=GGGCCGCGGGCGGGGGC=GC1=GGGGGJGGCCGJJCGGGJJJCGGG8CCGGGCJGJGJJGCCGCJJJJJJJJJJGCGJJJGJJGJGGGGGCGGGG=CC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-38 83 9 275900 60 150M = 275854 -196 ATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGA GCGCCGCGGGCGGGGGGGCGGCGCG8CGCGGGG8GGCGGGCCCCG8CC=JGCGGGGGGCGGGGCGCCGC=GCCCGGJGGGCGGGCJGCCJJGJG=GGCJJJGGJCGJCGCGJJJC=JJGJCJGJGJJGJJJ=JJJ1GGGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-6 147 9 275903 60 150M = 275846 -207 GCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCA CG8GCGGGCCCCGGCGCGGGGCCGGGCGG8CG=G=GCCGCGG=1CJ8JCCGCGGGGGCGGGGGGCGG=G=8GCGJG=GGGGGGJGCCGGJJGG=G=CJ8=JJJJGG=JJJJJGJJGJGJJGJJJJJCCCJJJGGJJJG1GGG1GGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-70 83 9 275911 60 150M = 275874 -187 TGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGC CGGGCGGGCGGGCCGGGG=GGG8GCGGG8GGCGGGCGGCGGGCGGGGG=JGGGGGCGCGGGGGCGGGGCGCG1GGGGCJC8GG=JGGJJCCCJJGGGGJGJGJGGJJGGJJJJJGCJJJJGGJJGJJGJJJGGGJJJGGGGCGGGGG=CC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-36 147 9 275919 60 150M = 275872 -197 AAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGCCAGAGGTC C=GGGGGGCCGGGGGGGGG=GGCCGCGGGC1GCGC1GCGGCCGJJ(CCG8GCCGGGCCGGGC=CC1CG=CGCCGGG=CGGGGGGGGCGGGGGJ==JJJJJ1CJJJGJGGJCGCJGJGJGJJJJ=GG1CJJCGJG1GC=GGGCGCGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-56 147 9 275928 60 150M = 275885 -193 CATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGCCAGAGGTCCATCTCGCT CCGGGCGCGCGGGCG=CCCGGCGCGGGGC=CGGCGGCCGCGGGJJJJCCGCCG(GCCCCCGGCCGGG=G8GGGGGGCC=C=CGGJGJJJGC=JGGJJJGJGJ1JJJGC=JJJG=JCJJJJJJJ=JJGGGJJJCGJJJGGGGGCGG=GCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-74 77 * 0 0 * * 0 0 TCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTC CC11GGGGGGGGGGCCJJJGCGJJGJJJJJGGGGGGJJJGGJG==GCJCJ=GGJJGGJJGGCJGG=GGGGGJGGJGC=GC=GGGCGGGCGGGGCCGCGGGJCGC=GGC8CGCGCGGGGGGCGCC1GGCGCC=GCCGCGGC8GCGGGCCCG NH:i:0 HI:i:0 AS:i:155 nM:i:2 uT:A:1 +BCR-ABL1-74 141 * 0 0 * * 0 0 CATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAGGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAG CCCGGGGGGCGCGJGGJJGGJGJJJGJGGJJGGJGJJ1=JCJJGGGJJJJGGGJGCCJGGJGG=J1JG8JGCGGGJG=GC1CGCCGGCG(GGCGGCGGGGGCJC1CCGC==CCGGGGCGGCGGGCCGGCGCGC8CCCCGGG=GGGC=GGG NH:i:0 HI:i:0 AS:i:155 nM:i:2 uT:A:1 +BCR-ABL1-66 77 * 0 0 * * 0 0 TCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTCAGAAACCCATAGAG CCC=GGGGCGGGGJJJJJGJJJJ=JJJGJJ1GJJGJJJJJGJJJJJGGGGCGJJGGGJJJGGCGGGGJGCGG1JCGGG=GCCGCG=GC=G=GCCGGGGG8JGGGGGGGGGGGG=GGCGGC8GGCCGGGC=GGGGGGGGG=CGG=8GGCCG NH:i:0 HI:i:0 AS:i:159 nM:i:0 uT:A:1 +BCR-ABL1-66 141 * 0 0 * * 0 0 CATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAG CCCGGGGGGGGGGGGJ=JGJJJJJJJGGJJCCCJGJJ1JJJGCJGGGGJJJJ=GGGJGJGC(GGGGJGGGJG1=GGGGGGGG=G=C=GG8CC8GGGGGCCCCJCCCJGCG=GGCCGGCGGCGGCG==1GCCGGC1GGGGGCGGGGGGCGG NH:i:0 HI:i:0 AS:i:159 nM:i:0 uT:A:1 +BCR-ABL1-58 77 * 0 0 * * 0 0 ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGG CCCGGCGGGGGGGGJJJJJGJJGJGJGJGJJJJJJJJJCJGJJJJGCG=8GGGJGJGGCGGJGCGJJJCJGGG=CGCCGGCCGGGCGCGGGCGCG1GGGCCCGGGGCG8GCCC=C8CGCGG=CCCGCCCCGGG=CCGGCGGGCGGGGGCG NH:i:0 HI:i:0 AS:i:185 nM:i:3 uT:A:1 +BCR-ABL1-58 141 * 0 0 * * 0 0 TTGGGGTCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATTCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATG CCCGGGGGGGGGGJJJJJJGJGJJJGGJ=JJJJJJJJGC=GJJGGJJGJJGG1GCJGGGG=JGGG8C=GCCGC==GGGCGGGGGG=GGG=(G=CCGCCGGGGCJJJJGGGC8GCGCGCG8CGGCCGGGCGCGCGG8CCGG8CGGGGGGGG NH:i:0 HI:i:0 AS:i:185 nM:i:3 uT:A:1 +BCR-ABL1-24 77 * 0 0 * * 0 0 CGCAGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGGCTGAGTGAAG CC11GCGGGGGGGJCGJGJJCCJJJJGJJJJGJJGGJJJCJJJG8JJJ1GJ=JGGGGJJJCG=8GGCGCCGGGCCGGGCGGGGCGGGGCCGCGGCCGGG=J1GCCC1(CCGGCGGGCCGCGGGCGGGGC=GGCGCCGCC1GCGGGGGCGG NH:i:0 HI:i:0 AS:i:154 nM:i:3 uT:A:1 +BCR-ABL1-24 141 * 0 0 * * 0 0 TTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTCAGAA C=CCGGGGGGGGCJ1GGJJJJ1JJJJJGJJ=GJJG8GGJ=GJGJJGJJGGGCGJGCGGGCGGG8GG=GJJGCG1GCGGJGCCGGCGGGCCGGGCG8GGGGG8C1==CGGCCCGCGGGGC8GCGGG8GGGCGCCGCCGCGGGCGGGGGGCG NH:i:0 HI:i:0 AS:i:154 nM:i:3 uT:A:1 +BCR-ABL1-10 77 * 0 0 * * 0 0 AGGTTGGGGTCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACG CC=GGGGGGGGGG1GJJJJJCJJJJJJJJJJJGJ=GJJJGCJJJJCJGJGCJGJJJGGJJJGGCCGGJGC=GGJ1C8GGGGGGCGCCGGGGGGCGGGCGCCCG1GGCGCGCGGGCC8GCGCGCGC8CCCGCGCGGGGGCGGGGGCGGCGG NH:i:0 HI:i:0 AS:i:181 nM:i:2 uT:A:1 +BCR-ABL1-10 141 * 0 0 * * 0 0 ATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGA 1CCGGCGGGGGG1GGJJJGCC1JJJJCCG=JGGJJGJJJ=GGGGGJJGGGGGGC1J=CJGCGGGGCGC(CGGGGG=GGGGG(G=CGGCGGGGCCCGC=CCCCJJCC8G1GGGGCGGGGGGCGCGGGGGGGCG=GGCCGCCGCC1G=GGGG NH:i:0 HI:i:0 AS:i:181 nM:i:2 uT:A:1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cytobands.tsv Wed Jul 27 11:24:44 2022 +0000 @@ -0,0 +1,5 @@ +contig start end name giemsa +22 1 40586 q11.22 gpos25 +22 40586 269079 q11.23 gneg +9 1 21036 q34.11 gneg +9 21036 515509 q34.12 gpos25
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fusions.tsv Wed Jul 27 11:24:44 2022 +0000 @@ -0,0 +1,2 @@ +#gene1 gene2 strand1(gene/fusion) strand2(gene/fusion) breakpoint1 breakpoint2 site1 site2 type split_reads1 split_reads2 discordant_mates coverage1 coverage2 confidence reading_frame tags retained_protein_domains closest_genomic_breakpoint1 closest_genomic_breakpoint2 gene_id1 gene_id2 transcript_id1 transcript_id2 direction1 direction2 filters fusion_transcript peptide_sequence read_identifiers +BCR ABL1 +/+ +/+ 22:230999 9:275100 CDS/splice-site CDS/splice-site translocation 1 3 0 3 8 low in-frame . Bcr-Abl_oncoprotein_oligomerisation_domain(100%),C2_domain(100%),RhoGEF_domain(100%)|F-actin_binding(100%),Protein_kinase_domain(100%),SH2_domain(100%),SH3_domain(100%) . . ENSG00000186716 ENSG00000097007 ENST00000305877 ENST00000372348 downstream upstream . AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAG___ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA|AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAG___GTGAAAAGCTCCGGG SFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFLNVIVHSATGFKQSS|kALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLR BCR-ABL1-4,BCR-ABL1-28,BCR-ABL1-60,BCR-ABL1-76
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein_domains.gff3 Wed Jul 27 11:24:44 2022 +0000 @@ -0,0 +1,83 @@ +9 pfam protein_domain 33502 33541 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 33992 34063 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 35324 35381 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 37391 37409 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 37479 37553 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 38833 38931 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 41390 41413 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 41489 41494 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 43744 43846 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 44647 44729 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 47496 47541 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 51664 51812 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 102331 102396 0 + . Name=Zinc finger%2C C2H2 type;color=#80FF00;gene_id=ENSG00000130711;gene_name=PRDM12;protein_domain_id=PF00096 +9 pfam protein_domain 102412 102480 0 + . Name=C2H2-type zinc finger;color=#80FF80;gene_id=ENSG00000130711;gene_name=PRDM12;protein_domain_id=PF13894 +9 pfam protein_domain 114903 114949 0 + . Name=Exosome complex exonuclease RRP4 N-terminal region;color=#FF0000;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF14382 +9 pfam protein_domain 116528 116596 0 + . Name=Exosome complex exonuclease RRP4 N-terminal region;color=#FF0000;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF14382 +9 pfam protein_domain 121951 121971 0 + . Name=KH domain;color=#000080;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF15985 +9 pfam protein_domain 123179 123300 0 + . Name=KH domain;color=#000080;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF15985 +9 pfam protein_domain 275219 275273 0 + . Name=SH3 domain;color=#FF0000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00018 +9 pfam protein_domain 275837 275922 0 + . Name=SH3 domain;color=#FF0000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00018 +9 pfam protein_domain 275962 276132 0 + . Name=SH2 domain;color=#80FFFF;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00017 +9 pfam protein_domain 283799 283855 0 + . Name=SH2 domain;color=#80FFFF;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00017 +9 pfam protein_domain 283973 284071 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 293165 293249 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 293896 294073 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 295904 296088 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 299451 299603 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 301104 301156 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 306405 306716 0 + . Name=F-actin binding;color=#800000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF08919 +9 pfam protein_domain 314470 314862 0 - . Name=Orexigenic neuropeptide Qrfp/P518 ;color=#808000;gene_id=ENSG00000188710;gene_name=QRFP;protein_domain_id=PF11109 +9 pfam protein_domain 325106 325108 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 325118 325359 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 326270 326449 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 332828 332924 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 344780 344908 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 430353 430623 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055 +9 pfam protein_domain 447321 447625 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055 +9 pfam protein_domain 453081 453209 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055 +9 pfam protein_domain 457203 457334 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 459902 460054 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 460070 460088 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 460167 460282 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 462677 462771 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 466560 466608 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 470157 470166 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052 +9 pfam protein_domain 473527 473719 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052 +9 pfam protein_domain 473886 474001 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052 +9 pfam protein_domain 477965 478038 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052 +9 pfam protein_domain 478042 478107 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 478144 478183 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 482071 482168 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 482175 482259 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 487996 488060 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 488076 488222 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 489116 489262 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 489945 490067 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 490710 490856 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +22 pfam protein_domain 2420 2524 0 - . Name=Armadillo/beta-catenin-like repeat;color=#000080;gene_id=ENSG00000100218;gene_name=RSPH14;protein_domain_id=PF00514 +22 pfam protein_domain 36321 37004 0 + . Name=G-protein alpha subunit;color=#80FFFF;gene_id=ENSG00000128266;gene_name=GNAZ;protein_domain_id=PF00503 +22 pfam protein_domain 63673 63981 0 + . Name=G-protein alpha subunit;color=#80FFFF;gene_id=ENSG00000128266;gene_name=GNAZ;protein_domain_id=PF00503 +22 pfam protein_domain 90736 90740 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 93060 93112 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 93619 93720 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 96554 96622 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 98578 98629 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 99484 99565 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 99749 99839 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 101465 101502 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 121553 121771 0 + . Name=Bcr-Abl oncoprotein oligomerisation domain;color=#FF0000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF09036 +22 pfam protein_domain 201581 201640 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 201941 202126 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 208994 209101 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 212118 212178 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 213667 213719 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 214220 214312 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 230954 230999 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168 +22 pfam protein_domain 233127 233224 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168 +22 pfam protein_domain 235610 235741 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168 +22 pfam protein_domain 250010 250018 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168 +22 pfam protein_domain 252302 252422 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620 +22 pfam protein_domain 253473 253607 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620 +22 pfam protein_domain 254554 254659 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620 +22 pfam protein_domain 255138 255228 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Jul 27 11:24:44 2022 +0000 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jul 27 11:24:44 2022 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>