Mercurial > repos > trinity_ctat > ctat_mutations
changeset 2:c15d9049ab81 draft
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations-7cf8f5889a4d/ctat_mutations.xml Wed Nov 14 12:20:23 2018 -0500 @@ -0,0 +1,68 @@ +<tool id="ctat_mutations" name="ctat_mutations" version="1.0.0" profile="17.05"> + <description>Mutation Pipeline for calling SNPs and variants</description> + <requirements> + <requirement type="package" version="2.0.1">ctat-mutations</requirement> + </requirements> + <command detect_errors="default"> + <![CDATA[ + ctat_mutations \ + --plot \ + --out_dir varcalling.outdir \ + --threads 8 \ + --variant_filtering_mode GATK \ + --left "$left" \ + --right "$right" \ + --genome_lib_dir "${genome_resource_lib.fields.path}" \ + --variant_call_mode GATK \ + --tissue_type "$tissue_type" \ + --email "$cravat_email" + ]]> + </command> + <inputs> + <param format="fastq" name="left" type="data" label="Left/Forward strand reads" help="Left read"/> + <param format="fastq" name="right" type="data" label="Right/Reverse strand reads" help="Right read"/> + <param name="tissue_type" type="select" label="Select a pathology" help="If you don't know, just choose 'General Purpose'"> + <options from_data_table="ctat_cravat_tissues"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + <param name="genome_resource_lib" type="select" label="Select a reference genome"> + <options from_data_table="ctat_genome_resource_libs"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + <param name="cravat_email" type="text" label="CRAVAT email" help="CRAVAT registered email id"/> + <section name="adv" title="This service uses the GATK4. GATK4 is licensed by the Broad Institute and is made available to academic users of this service for non-commercial use only. The full text of the license is available here: https://www.broadinstitute.org/gatk/about/license.html. For more information about GATK and full documentation, please visit the GATK website: https://www.broadinstitute.org." expanded="False"> + </section> + </inputs> + <outputs> + <data format="tabular" name="cancertab" label="${tool.name} on ${on_string}: Cancer Tab" from_work_dir="varcalling.outdir/cancer.tab"/> + <data format="vcf" name="cancerVariants" label="${tool.name} on ${on_string}: Cancer VCF" from_work_dir="varcalling.outdir/cancer.vcf"/> + <data format="vcf" name="allVariants" label="${tool.name} on ${on_string}: All Variants VCF" from_work_dir="varcalling.outdir/variants.vcf"/> + <data format="bam" name="bamfile" label="Bam used in haplotype calling" from_work_dir="varcalling.outdir/misc/recalibrated.bam"/> + <data format="txt" name="cravat" label="Annotated (lightly filtered) VCF file" from_work_dir="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/> + </outputs> + <tests> + <test> + <param name="left" value="reads_1.fastq.gz"/> + <param name="right" value="reads_2.fastq.gz"/> + <param name="tissue_type" value="Other"/> + <output name="cancertab" file="varcalling.outdir/cancer.tab" /> + <output name="cancerVariants" file="varcalling.outdir/cancer.vcf" /> + <output name="allVariants" file="varcalling.outdir/variants.vcf" /> + <output name="bamfile" file="varcalling.outdir/misc/recalibrated.bam" /> + <output name="cravat" file="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/> + </test> + </tests> + <help> + +.. class:: warningmark + +Mutation detection in RNA-Seq highlights the GATK Best Practices in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT. + + </help> + <citations> + </citations> +</tool>
Binary file ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/annotated_min_filtered.vcf.gz has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/cancer.tab Wed Nov 14 12:20:23 2018 -0500 @@ -0,0 +1,14 @@ +CHROM POS REF ALT GENE DP QUAL MQ SAO NSF NSM NSN TUMOR TISSUE COSMIC_ID KGPROD RS PMC CHASM_PVALUE CHASM_FDR VEST_PVALUE VEST_FDR +chr5 474989 A G LOC100288152,SLC9A3 4 96.03 60 NA NA NA NA carcinoma_--_NS urinary_tract COSM4006021 NA NA NA 0.1114 0.2 0.96802 1 +chr5 181224474 G A TRIM41 45 349.77 60 NA NA NA NA NA NA NA NA NA NA 0.0694 0.15 0.48052 1 +chr8 143923759 G A PLEC 66 838.77 60 NA NA NA NA carcinoma_--_adenocarcinoma large_intestine COSM3750086 NA NA NA 0.0344 0.1 0.84202 1 +chr12 56420869 G A TIMELESS 48 384.77 60 NA NA NA NA carcinoma_--_adenocarcinoma large_intestine COSM3753397 NA NA NA 0.0744 0.15 0.18439 0.95 +chr17 7673767 C T TP53 61 1848.77 60 NA NA NA NA Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS bone COSM3717625 NA NA NA 0 0.05 0.01447 0.15 +chr17 7676154 G C TP53 80 2161.77 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3766193 NA NA NA 0.087 0.15 0.52717 1 +chr17 43071077 T C BRCA1 4 92.03 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3755560 NA NA NA 0.0372 0.1 0.3446 1 +chr17 43091983 T C BRCA1 4 84.03 60 NA NA NA NA haemangioblastoma_--_NS soft_tissue COSM3755561 NA NA NA 0.0002 0.05 0.64447 1 +chr17 43092919 G A BRCA1 2 33.74 60 NA NA NA NA carcinoma_--_NS prostate COSM3755564 NA NA NA 0.0004 0.05 0.33539 1 +chr17 43093454 C T BRCA1 11 425.77 60 NA NA NA NA rhabdomyosarcoma_--_embryonal soft_tissue COSM4989394 NA NA NA 0.0014 0.05 0.51068 1 +chr19 39177761 G C PAK4 106 1134.77 60 NA NA NA NA NA NA NA NA NA NA 0.0004 0.05 0.01093 0.15 +chr19 47271515 T C CCDC9 12 336.77 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3721172 NA NA NA 0.093 0.15 0.97622 1 +chr20 46687147 C T TP53RK 26 423.77 60 NA NA NA NA carcinoma_--_ductal_carcinoma pancreas COSM3758608 NA NA NA 0.0834 0.15 0.88584 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/cancer.vcf Wed Nov 14 12:20:23 2018 -0500 @@ -0,0 +1,87 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##FILTER=<ID=FS,Description="FS > 30.0"> +##FILTER=<ID=LowQual,Description="Low quality"> +##FILTER=<ID=QD,Description="QD < 2.0"> +##FILTER=<ID=SnpCluster,Description="SNPs found in clusters"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --recover-dangling-heads true --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20.0 --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --input /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --emit-ref-confidence NONE --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.10.0,Date="October 29, 2018 1:03:15 PM EDT"> +##GATKCommandLine=<ID=VariantFiltration,CommandLine="VariantFiltration --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants_initial_filtering.vcf --filter-expression FS > 30.0 --filter-expression QD < 2.0 --filter-name FS --filter-name QD --cluster-size 3 --cluster-window-size 35 --variant /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --mask-extension 0 --mask-name Mask --filter-not-in-mask false --missing-values-evaluate-as-failing false --invalidate-previous-filters false --invert-filter-expression false --invert-genotype-filter-expression false --set-filtered-genotype-to-no-call false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version=4.0.10.0,Date="October 29, 2018 1:15:13 PM EDT"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele in the same order as listed"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency for each ALT allele in the same order as listed"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> +##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> +##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> +##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> +##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC) for each ALT allele in the same order as listed"> +##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF) for each ALT allele in the same order as listed"> +##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> +##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> +##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> +##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> +##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr2,length=242193529> +##contig=<ID=chr3,length=198295559> +##contig=<ID=chr4,length=190214555> +##contig=<ID=chr5,length=181538259> +##contig=<ID=chr6,length=170805979> +##contig=<ID=chr7,length=159345973> +##contig=<ID=chr8,length=145138636> +##contig=<ID=chr9,length=138394717> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr15,length=101991189> +##contig=<ID=chr16,length=90338345> +##contig=<ID=chr17,length=83257441> +##contig=<ID=chr18,length=80373285> +##contig=<ID=chr19,length=58617616> +##contig=<ID=chr20,length=64444167> +##contig=<ID=chr21,length=46709983> +##contig=<ID=chr22,length=50818468> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##contig=<ID=chrM,length=16569> +##source=HaplotypeCaller +##source=VariantFiltration +##SnpEffVersion="4.1k (build 2015-09-07), by Pablo Cingolani" +##SnpEffCmd="SnpEff -nostats -noLof -no-downstream -no-upstream hg38 " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##INFO=<ID=GENE,Number=.,Type=String,Description="The name of the gene/s in the genomic region of the SNP as annotated by SNPeff"> +##INFO=<ID=COSMIC_ID,Number=.,Type=String,Description="COSMIC mutation id (unique)."> +##INFO=<ID=TISSUE,Number=.,Type=String,Description="The primary tissue/cancer and subtype from which the sample originated."> +##INFO=<ID=TUMOR,Number=.,Type=String,Description="The histological classification of the sample."> +##INFO=<ID=FATHMM,Number=.,Type=String,Description="FATHMM (Functional Analysis through Hidden Markov Models). 'Pathogenic':Cancer or damaging 'Neutral':Passanger or Tolerated."> +##INFO=<ID=SOMATIC,Number=.,Type=String,Description="Information on whether the sample was reported to be Confirmed Somatic. 'Confirmed somatic':if the mutation has been confimed to be somatic in the experiment by sequencing both the tumour and a matched normal from the same patient 'Previously Observed':when the mutation has been reported as somatic previously but not in current paper 'variant of unknown origin':when the mutation is known to be somatic but the tumour was sequenced without a matched normal"> +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=annotate --output-type z --annotations /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/cosmic.vcf.gz --columns INFO/COSMIC_ID,INFO/TISSUE,INFO/TUMOR,INFO/FATHMM,INFO/SOMATIC --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/variants_annotated.vcf.gz /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz; Date=Mon Oct 29 13:22:17 2018 +##INFO=<ID=CHASM_PVALUE,Number=.,Type=Float,Description="CHASM cancer driver p-value (missense) generated by CRAVAT"> +##INFO=<ID=CHASM_FDR,Number=.,Type=Float,Description="CHASM cancer driver FDR (missense)"> +##INFO=<ID=VEST_PVALUE,Number=.,Type=Float,Description="VEST pathogenicity p-value (non-silent)"> +##INFO=<ID=VEST_FDR,Number=.,Type=Float,Description="VEST pathogenicity FDR (non-silent)"> +##bcftools_annotateCommand=annotate --annotations /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/Variant_result_updated.tsv.gz -h /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/header/cravat_annotation.txt --columns CHROM,POS,CHASM_PVALUE,CHASM_FDR,VEST_PVALUE,VEST_FDR --output-type z --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/variants_initial_filtering_clean_snp_RNAedit_cosmic_filtered_cravat_annotated_coding.vcf.gz /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/variants_initial_filtering_clean_snp_RNAedit_cosmic_filtered.vcf; Date=Mon Oct 29 13:23:53 2018 +##bcftools_annotateCommand=annotate --annotations /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/Variant_non_coding_result_updated.tsv.gz -h /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/header/cravat_annotation.txt --columns CHROM,POS,CHASM_PVALUE,CHASM_FDR,VEST_PVALUE,VEST_FDR --output-type z --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/annotated_min_filtered.vcf.gz /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/variants_initial_filtering_clean_snp_RNAedit_cosmic_filtered_cravat_annotated_coding.vcf.gz; Date=Mon Oct 29 13:23:53 2018 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_1_fastq +chr5 474989 . A G 96.03 PASS GENE=LOC100288152,SLC9A3;AC=2;AF=1;AN=2;DP=4;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=24.01;SOR=1.609;ANN=G|missense_variant|MODERATE|SLC9A3|SLC9A3|transcript|NM_004174.2|Coding|16/17|c.2395T>C|p.Cys799Arg|2507/2777|2395/2505|799/834||,G|missense_variant|MODERATE|SLC9A3|SLC9A3|transcript|NM_001284351.1|Coding|16/17|c.2368T>C|p.Cys790Arg|2480/2750|2368/2478|790/825||,G|intron_variant|MODIFIER|LOC100288152|LOC100288152|transcript|NR_125375.1|Noncoding|1/6|n.165-148A>G||||||;COSMIC_ID=COSM4006021;TISSUE=urinary_tract;TUMOR=carcinoma_--_NS;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.1114;CHASM_FDR=0.2;VEST_PVALUE=0.96802;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:124,12,0 +chr5 181224474 . G A 349.77 PASS GENE=TRIM41;AC=1;AF=0.5;AN=2;BaseQRankSum=0.32;DP=45;ExcessHet=3.0103;FS=1.237;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=7.77;ReadPosRankSum=0.504;SOR=0.945;ANN=A|missense_variant|MODERATE|TRIM41|TRIM41|transcript|NM_033549.4|Coding|1/6|c.475G>A|p.Glu159Lys|1212/3663|475/1893|159/630||,A|missense_variant|MODERATE|TRIM41|TRIM41|transcript|NM_201627.2|Coding|1/8|c.475G>A|p.Glu159Lys|1212/2723|475/1557|159/518||,A|non_coding_exon_variant|MODIFIER|TRIM41|TRIM41|transcript|NR_045218.1|Noncoding|1/7|n.1212G>A||||||;CHASM_PVALUE=0.0694;CHASM_FDR=0.15;VEST_PVALUE=0.48052;VEST_FDR=1 GT:AD:DP:GQ:PL 0/1:28,17:45:99:378,0,717 +chr8 143923759 . G A 838.77 PASS GENE=PLEC;AC=1;AF=0.5;AN=2;BaseQRankSum=-0.63;DP=66;ExcessHet=3.0103;FS=0.94;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=12.71;ReadPosRankSum=0.567;SOR=0.82;ANN=A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201380.3|Coding|31/32|c.6581C>T|p.Ala2194Val|6751/15255|6581/14055|2194/4684||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201384.2|Coding|31/32|c.6170C>T|p.Ala2057Val|6299/14803|6170/13644|2057/4547||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201383.2|Coding|31/32|c.6182C>T|p.Ala2061Val|6191/14695|6182/13656|2061/4551||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201382.3|Coding|31/32|c.6170C>T|p.Ala2057Val|6238/14742|6170/13644|2057/4547||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201381.2|Coding|31/32|c.6074C>T|p.Ala2025Val|6148/14652|6074/13548|2025/4515||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201379.2|Coding|31/32|c.6104C>T|p.Ala2035Val|6253/14757|6104/13578|2035/4525||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201378.3|Coding|31/32|c.6128C>T|p.Ala2043Val|6185/14689|6128/13602|2043/4533||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_000445.4|Coding|32/33|c.6251C>T|p.Ala2084Val|6300/14804|6251/13725|2084/4574||;COSMIC_ID=COSM3750086;TISSUE=large_intestine;TUMOR=carcinoma_--_adenocarcinoma;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0344;CHASM_FDR=0.1;VEST_PVALUE=0.84202;VEST_FDR=1 GT:AD:DP:GQ:PL 0/1:31,35:66:99:867,0,736 +chr12 56420869 . G A 384.77 PASS GENE=TIMELESS;AC=1;AF=0.5;AN=2;BaseQRankSum=2.348;DP=48;ExcessHet=3.0103;FS=4.262;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=8.02;ReadPosRankSum=0.096;SOR=0.674;ANN=A|missense_variant|MODERATE|TIMELESS|TIMELESS|transcript|NM_003920.3|Coding|25/29|c.3053C>T|p.Pro1018Leu|3221/5138|3053/3627|1018/1208||;COSMIC_ID=COSM3753397;TISSUE=large_intestine;TUMOR=carcinoma_--_adenocarcinoma;FATHMM=PATHOGENIC;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0744;CHASM_FDR=0.15;VEST_PVALUE=0.18439;VEST_FDR=0.95 GT:AD:DP:GQ:PL 0/1:30,18:48:99:413,0,759 +chr17 7673767 . C T 1848.77 PASS GENE=TP53;AC=2;AF=1;AN=2;DP=61;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=30.31;SOR=1.609;ANN=T|missense_variant|MODERATE|TP53|TP53|transcript|NM_000546.5|Coding|8/11|c.853G>A|p.Glu285Lys|1055/2591|853/1182|285/393||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126115.1|Coding|4/7|c.457G>A|p.Glu153Lys|735/2271|457/786|153/261||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126116.1|Coding|4/8|c.457G>A|p.Glu153Lys|735/2404|457/630|153/209||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126117.1|Coding|4/8|c.457G>A|p.Glu153Lys|735/2331|457/645|153/214||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276697.1|Coding|4/7|c.376G>A|p.Glu126Lys|735/2271|376/705|126/234||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276698.1|Coding|4/8|c.376G>A|p.Glu126Lys|735/2404|376/549|126/182||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276699.1|Coding|4/8|c.376G>A|p.Glu126Lys|735/2331|376/564|126/187||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126112.2|Coding|8/11|c.853G>A|p.Glu285Lys|1052/2588|853/1182|285/393||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126113.2|Coding|8/12|c.853G>A|p.Glu285Lys|1055/2651|853/1041|285/346||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126114.2|Coding|8/12|c.853G>A|p.Glu285Lys|1055/2724|853/1026|285/341||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126118.1|Coding|7/10|c.736G>A|p.Glu246Lys|1172/2708|736/1065|246/354||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276695.1|Coding|8/12|c.736G>A|p.Glu246Lys|1055/2651|736/924|246/307||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276696.1|Coding|8/12|c.736G>A|p.Glu246Lys|1055/2724|736/909|246/302||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276760.1|Coding|8/11|c.736G>A|p.Glu246Lys|1055/2591|736/1065|246/354||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276761.1|Coding|8/11|c.736G>A|p.Glu246Lys|1052/2588|736/1065|246/354||;COSMIC_ID=COSM3717625;TISSUE=bone;TUMOR=Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS;FATHMM=PATHOGENIC;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0;CHASM_FDR=0.05;VEST_PVALUE=0.01447;VEST_FDR=0.15 GT:AD:DP:GQ:PL 1/1:0,61:61:99:1877,183,0 +chr17 7676154 . G C 2161.77 PASS GENE=TP53;AC=2;AF=1;AN=2;BaseQRankSum=3.225;DP=80;ExcessHet=3.0103;FS=14.289;MLEAC=2;MLEAF=1;MQ=60;MQRankSum=0;QD=27.02;ReadPosRankSum=-2.023;SOR=0.642;ANN=C|missense_variant|MODERATE|TP53|TP53|transcript|NM_000546.5|Coding|4/11|c.215C>G|p.Pro72Arg|417/2591|215/1182|72/393||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126112.2|Coding|4/11|c.215C>G|p.Pro72Arg|414/2588|215/1182|72/393||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126113.2|Coding|4/12|c.215C>G|p.Pro72Arg|417/2651|215/1041|72/346||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126114.2|Coding|4/12|c.215C>G|p.Pro72Arg|417/2724|215/1026|72/341||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126118.1|Coding|3/10|c.98C>G|p.Pro33Arg|534/2708|98/1065|33/354||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276695.1|Coding|4/12|c.98C>G|p.Pro33Arg|417/2651|98/924|33/307||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276696.1|Coding|4/12|c.98C>G|p.Pro33Arg|417/2724|98/909|33/302||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276760.1|Coding|4/11|c.98C>G|p.Pro33Arg|417/2591|98/1065|33/354||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276761.1|Coding|4/11|c.98C>G|p.Pro33Arg|414/2588|98/1065|33/354||;COSMIC_ID=COSM3766193;TISSUE=haematopoietic_and_lymphoid_tissue;TUMOR=haematopoietic_neoplasm_--_acute_myeloid_leukaemia;FATHMM=NEUTRAL;SOMATIC=Reported_in_another_cancer_sample_as_somatic;CHASM_PVALUE=0.087;CHASM_FDR=0.15;VEST_PVALUE=0.52717;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:4,76:80:99:2190,183,0 +chr17 43071077 . T C 92.03 PASS GENE=BRCA1;AC=2;AF=1;AN=2;DP=4;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=23.01;SOR=3.258;ANN=C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|16/24|c.4900A>G|p.Ser1634Gly|5132/7270|4900/5655|1634/1884||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007298.3|Coding|14/22|c.1525A>G|p.Ser509Gly|1544/3682|1525/2280|509/759||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|14/22|c.4696A>G|p.Ser1566Gly|4977/7115|4696/5451|1566/1816||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007299.3|Coding|15/22|c.1525A>G|p.Ser509Gly|1719/3783|1525/2100|509/699||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|15/23|c.4837A>G|p.Ser1613Gly|5069/7207|4837/5592|1613/1863||,C|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|15/23|n.4973A>G||||||;COSMIC_ID=COSM3755560;TISSUE=haematopoietic_and_lymphoid_tissue;TUMOR=haematopoietic_neoplasm_--_acute_myeloid_leukaemia;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0372;CHASM_FDR=0.1;VEST_PVALUE=0.3446;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:120,12,0 +chr17 43091983 . T C 84.03 PASS GENE=BRCA1;AC=2;AF=1;AN=2;DP=4;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=21.01;SOR=0.693;ANN=C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.3548A>G|p.Lys1183Arg|3780/7270|3548/5655|1183/1884||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.3407A>G|p.Lys1136Arg|3688/7115|3407/5451|1136/1816||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.3548A>G|p.Lys1183Arg|3780/7207|3548/5592|1183/1863||,C|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.788-951A>G||||||,C|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.788-951A>G||||||,C|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.3684A>G||||||;COSMIC_ID=COSM3755561;TISSUE=soft_tissue;TUMOR=haemangioblastoma_--_NS;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0002;CHASM_FDR=0.05;VEST_PVALUE=0.64447;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:112,12,0 +chr17 43092919 . G A 33.74 PASS GENE=BRCA1;AC=2;AF=1;AN=2;DP=2;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=16.87;SOR=2.303;ANN=A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.2612C>T|p.Pro871Leu|2844/7270|2612/5655|871/1884||,A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.2471C>T|p.Pro824Leu|2752/7115|2471/5451|824/1816||,A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.2612C>T|p.Pro871Leu|2844/7207|2612/5592|871/1863||,A|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T||||||,A|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.787+1825C>T||||||,A|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.2748C>T||||||;COSMIC_ID=COSM3755564;TISSUE=prostate;TUMOR=carcinoma_--_NS;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0004;CHASM_FDR=0.05;VEST_PVALUE=0.33539;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 +chr17 43093454 . C T 425.77 PASS GENE=BRCA1;AC=2;AF=1;AN=2;DP=11;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=31.78;SOR=1.27;ANN=T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.2077G>A|p.Asp693Asn|2309/7270|2077/5655|693/1884||,T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.1936G>A|p.Asp646Asn|2217/7115|1936/5451|646/1816||,T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.2077G>A|p.Asp693Asn|2309/7207|2077/5592|693/1863||,T|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.787+1290G>A||||||,T|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.787+1290G>A||||||,T|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.2213G>A||||||;COSMIC_ID=COSM4989394;TISSUE=soft_tissue;TUMOR=rhabdomyosarcoma_--_embryonal;FATHMM=NEUTRAL;SOMATIC=Reported_in_another_cancer_sample_as_somatic;CHASM_PVALUE=0.0014;CHASM_FDR=0.05;VEST_PVALUE=0.51068;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,11:11:33:454,33,0 +chr19 39177761 . G C 1134.77 PASS GENE=PAK4;AC=1;AF=0.5;AN=2;BaseQRankSum=2.258;DP=106;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=10.71;ReadPosRankSum=1.397;SOR=0.654;ANN=C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014831.2|Coding|10/11|c.1572G>C|p.Met524Ile|2033/3064|1572/1776|524/591||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014832.1|Coding|8/9|c.1572G>C|p.Met524Ile|1734/2765|1572/1776|524/591||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014834.2|Coding|7/8|c.1113G>C|p.Met371Ile|1275/2306|1113/1317|371/438||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014835.1|Coding|8/9|c.1113G>C|p.Met371Ile|1348/2379|1113/1317|371/438||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_005884.3|Coding|9/10|c.1572G>C|p.Met524Ile|1807/2838|1572/1776|524/591||;CHASM_PVALUE=0.0004;CHASM_FDR=0.05;VEST_PVALUE=0.01093;VEST_FDR=0.15 GT:AD:DP:GQ:PL 0/1:58,48:106:99:1163,0,1435 +chr19 47271515 . T C 336.77 PASS GENE=CCDC9;AC=2;AF=1;AN=2;DP=12;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=28.06;SOR=2.67;ANN=C|missense_variant|MODERATE|CCDC9|CCDC9|transcript|NM_015603.2|Coding|12/12|c.1433T>C|p.Leu478Pro|1640/2078|1433/1596|478/531||;COSMIC_ID=COSM3721172;TISSUE=haematopoietic_and_lymphoid_tissue;TUMOR=haematopoietic_neoplasm_--_acute_myeloid_leukaemia;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.093;CHASM_FDR=0.15;VEST_PVALUE=0.97622;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,12:12:36:365,36,0 +chr20 46687147 . C T 423.77 PASS GENE=TP53RK;AC=1;AF=0.5;AN=2;BaseQRankSum=-0.26;DP=26;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=16.3;ReadPosRankSum=1.395;SOR=1.179;ANN=T|missense_variant|MODERATE|TP53RK|TP53RK|transcript|NM_033550.3|Coding|2/2|c.368G>A|p.Arg123Gln|591/3373|368/762|123/253||;COSMIC_ID=COSM3758608;TISSUE=pancreas;TUMOR=carcinoma_--_ductal_carcinoma;FATHMM=PATHOGENIC;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0834;CHASM_FDR=0.15;VEST_PVALUE=0.88584;VEST_FDR=1 GT:AD:DP:GQ:PL 0/1:8,18:26:99:452,0,165
Binary file ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/misc/recalibrated.bai has changed
Binary file ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/misc/recalibrated.bam has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/mutation_inspector.json Wed Nov 14 12:20:23 2018 -0500 @@ -0,0 +1,321 @@ +{ + "BAM": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam", + "BAM_INDEX": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bai", + "BED": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed", + "BED_INDEX": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed.idx", + "SAMPLE": "varcalling.outdir", + "SNV": [ + { + "ALT": "G", + "CHASM_FDR": "0.2", + "CHASM_PVALUE": "0.1114", + "CHROM": "chr5", + "COSMIC_ID": "COSM4006021", + "DP": "4", + "GENE": "LOC100288152,SLC9A3", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "474989", + "QUAL": "96.03", + "REF": "A", + "RS": "NA", + "SAO": "NA", + "TISSUE": "urinary_tract", + "TUMOR": "carcinoma_--_NS", + "VEST_FDR": "1", + "VEST_PVALUE": "0.96802" + }, + { + "ALT": "A", + "CHASM_FDR": "0.15", + "CHASM_PVALUE": "0.0694", + "CHROM": "chr5", + "COSMIC_ID": "NA", + "DP": "45", + "GENE": "TRIM41", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "181224474", + "QUAL": "349.77", + "REF": "G", + "RS": "NA", + "SAO": "NA", + "TISSUE": "NA", + "TUMOR": "NA", + "VEST_FDR": "1", + "VEST_PVALUE": "0.48052" + }, + { + "ALT": "A", + "CHASM_FDR": "0.1", + "CHASM_PVALUE": "0.0344", + "CHROM": "chr8", + "COSMIC_ID": "COSM3750086", + "DP": "66", + "GENE": "PLEC", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "143923759", + "QUAL": "838.77", + "REF": "G", + "RS": "NA", + "SAO": "NA", + "TISSUE": "large_intestine", + "TUMOR": "carcinoma_--_adenocarcinoma", + "VEST_FDR": "1", + "VEST_PVALUE": "0.84202" + }, + { + "ALT": "A", + "CHASM_FDR": "0.15", + "CHASM_PVALUE": "0.0744", + "CHROM": "chr12", + "COSMIC_ID": "COSM3753397", + "DP": "48", + "GENE": "TIMELESS", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "56420869", + "QUAL": "384.77", + "REF": "G", + "RS": "NA", + "SAO": "NA", + "TISSUE": "large_intestine", + "TUMOR": "carcinoma_--_adenocarcinoma", + "VEST_FDR": "0.95", + "VEST_PVALUE": "0.18439" + }, + { + "ALT": "T", + "CHASM_FDR": "0.05", + "CHASM_PVALUE": "0", + "CHROM": "chr17", + "COSMIC_ID": "COSM3717625", + "DP": "61", + "GENE": "TP53", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "7673767", + "QUAL": "1848.77", + "REF": "C", + "RS": "NA", + "SAO": "NA", + "TISSUE": "bone", + "TUMOR": "Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS", + "VEST_FDR": "0.15", + "VEST_PVALUE": "0.01447" + }, + { + "ALT": "C", + "CHASM_FDR": "0.15", + "CHASM_PVALUE": "0.087", + "CHROM": "chr17", + "COSMIC_ID": "COSM3766193", + "DP": "80", + "GENE": "TP53", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "7676154", + "QUAL": "2161.77", + "REF": "G", + "RS": "NA", + "SAO": "NA", + "TISSUE": "haematopoietic_and_lymphoid_tissue", + "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", + "VEST_FDR": "1", + "VEST_PVALUE": "0.52717" + }, + { + "ALT": "C", + "CHASM_FDR": "0.1", + "CHASM_PVALUE": "0.0372", + "CHROM": "chr17", + "COSMIC_ID": "COSM3755560", + "DP": "4", + "GENE": "BRCA1", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "43071077", + "QUAL": "92.03", + "REF": "T", + "RS": "NA", + "SAO": "NA", + "TISSUE": "haematopoietic_and_lymphoid_tissue", + "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", + "VEST_FDR": "1", + "VEST_PVALUE": "0.3446" + }, + { + "ALT": "C", + "CHASM_FDR": "0.05", + "CHASM_PVALUE": "0.0002", + "CHROM": "chr17", + "COSMIC_ID": "COSM3755561", + "DP": "4", + "GENE": "BRCA1", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "43091983", + "QUAL": "84.03", + "REF": "T", + "RS": "NA", + "SAO": "NA", + "TISSUE": "soft_tissue", + "TUMOR": "haemangioblastoma_--_NS", + "VEST_FDR": "1", + "VEST_PVALUE": "0.64447" + }, + { + "ALT": "A", + "CHASM_FDR": "0.05", + "CHASM_PVALUE": "0.0004", + "CHROM": "chr17", + "COSMIC_ID": "COSM3755564", + "DP": "2", + "GENE": "BRCA1", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "43092919", + "QUAL": "33.74", + "REF": "G", + "RS": "NA", + "SAO": "NA", + "TISSUE": "prostate", + "TUMOR": "carcinoma_--_NS", + "VEST_FDR": "1", + "VEST_PVALUE": "0.33539" + }, + { + "ALT": "T", + "CHASM_FDR": "0.05", + "CHASM_PVALUE": "0.0014", + "CHROM": "chr17", + "COSMIC_ID": "COSM4989394", + "DP": "11", + "GENE": "BRCA1", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "43093454", + "QUAL": "425.77", + "REF": "C", + "RS": "NA", + "SAO": "NA", + "TISSUE": "soft_tissue", + "TUMOR": "rhabdomyosarcoma_--_embryonal", + "VEST_FDR": "1", + "VEST_PVALUE": "0.51068" + }, + { + "ALT": "C", + "CHASM_FDR": "0.05", + "CHASM_PVALUE": "0.0004", + "CHROM": "chr19", + "COSMIC_ID": "NA", + "DP": "106", + "GENE": "PAK4", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "39177761", + "QUAL": "1134.77", + "REF": "G", + "RS": "NA", + "SAO": "NA", + "TISSUE": "NA", + "TUMOR": "NA", + "VEST_FDR": "0.15", + "VEST_PVALUE": "0.01093" + }, + { + "ALT": "C", + "CHASM_FDR": "0.15", + "CHASM_PVALUE": "0.093", + "CHROM": "chr19", + "COSMIC_ID": "COSM3721172", + "DP": "12", + "GENE": "CCDC9", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "47271515", + "QUAL": "336.77", + "REF": "T", + "RS": "NA", + "SAO": "NA", + "TISSUE": "haematopoietic_and_lymphoid_tissue", + "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", + "VEST_FDR": "1", + "VEST_PVALUE": "0.97622" + }, + { + "ALT": "T", + "CHASM_FDR": "0.15", + "CHASM_PVALUE": "0.0834", + "CHROM": "chr20", + "COSMIC_ID": "COSM3758608", + "DP": "26", + "GENE": "TP53RK", + "KGPROD": "NA", + "MQ": "60", + "NSF": "NA", + "NSM": "NA", + "NSN": "NA", + "PMC": "NA", + "POS": "46687147", + "QUAL": "423.77", + "REF": "C", + "RS": "NA", + "SAO": "NA", + "TISSUE": "pancreas", + "TUMOR": "carcinoma_--_ductal_carcinoma", + "VEST_FDR": "1", + "VEST_PVALUE": "0.88584" + } + ] +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/variants.vcf Wed Nov 14 12:20:23 2018 -0500 @@ -0,0 +1,79 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=LowQual,Description="Low quality"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --recover-dangling-heads true --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20.0 --output 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A G 96.03 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.01;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,4:4:12:124,12,0 +chr5 475231 . A T 66.28 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=22.09;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 +chr5 181223744 . T C 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.544;DP=14;ExcessHet=3.0103;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.41;ReadPosRankSum=-0.756;SOR=1.863 GT:AD:DP:GQ:PL 0/1:6,8:14:99:202,0,133 +chr5 181224474 . G A 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=45;ExcessHet=3.0103;FS=1.237;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=7.77;ReadPosRankSum=0.504;SOR=0.945 GT:AD:DP:GQ:PL 0/1:28,17:45:99:378,0,717 +chr8 143923488 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.260;DP=78;ExcessHet=3.0103;FS=4.540;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.06;ReadPosRankSum=0.137;SOR=0.307 GT:AD:DP:GQ:PL 0/1:45,33:78:99:735,0,1132 +chr8 143923759 . G A 838.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.630;DP=66;ExcessHet=3.0103;FS=0.940;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.71;ReadPosRankSum=0.567;SOR=0.820 GT:AD:DP:GQ:PL 0/1:31,35:66:99:867,0,736 +chr8 143924001 . C T 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=60;ExcessHet=3.0103;FS=4.714;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.16;ReadPosRankSum=0.323;SOR=1.525 GT:AD:DP:GQ:PL 0/1:38,22:60:99:758,0,1811 +chr8 143924022 . A G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.271;DP=58;ExcessHet=3.0103;FS=14.916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.13;ReadPosRankSum=0.674;SOR=2.948 GT:AD:DP:GQ:PL 0/1:40,18:58:99:616,0,1892 +chr12 56420869 . G A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.348;DP=48;ExcessHet=3.0103;FS=4.262;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.02;ReadPosRankSum=0.096;SOR=0.674 GT:AD:DP:GQ:PL 0/1:30,18:48:99:413,0,759 +chr12 56420872 . A G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.308;DP=46;ExcessHet=3.0103;FS=8.803;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.13;ReadPosRankSum=0.656;SOR=1.232 GT:AD:DP:GQ:PL 0/1:18,28:46:99:724,0,415 +chr12 56422138 . C T 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.718;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.10;ReadPosRankSum=-0.816;SOR=0.693 GT:AD:DP:GQ:PL 0/1:4,4:8:96:101,0,96 +chr17 7673767 . C T 1848.77 . AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.31;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,61:61:99:1877,183,0 +chr17 7675327 . C T 32.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.37;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:60,6,0 +chr17 7676154 . G C 2161.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=3.225;DP=80;ExcessHet=3.0103;FS=14.289;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=27.02;ReadPosRankSum=-2.023;SOR=0.642 GT:AD:DP:GQ:PL 1/1:4,76:80:99:2190,183,0 +chr17 43071077 . T C 92.03 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=23.01;SOR=3.258 GT:AD:DP:GQ:PL 1/1:0,4:4:12:120,12,0 +chr17 43082453 . A G 37.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=18.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 +chr17 43091983 . T C 84.03 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.01;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,4:4:12:112,12,0 +chr17 43092919 . G A 33.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 +chr17 43093220 . A G 278.77 . AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.88;SOR=4.804 GT:AD:DP:GQ:PL 1/1:0,10:10:30:307,30,0 +chr17 43093449 . G A 425.77 . AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.87;SOR=1.402 GT:AD:DP:GQ:PL 1/1:0,9:9:33:454,33,0 +chr17 43093454 . C T 425.77 . AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.78;SOR=1.270 GT:AD:DP:GQ:PL 1/1:0,11:11:33:454,33,0 +chr19 39177761 . G C 1134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.258;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.71;ReadPosRankSum=1.397;SOR=0.654 GT:AD:DP:GQ:PL 0/1:58,48:106:99:1163,0,1435 +chr19 39178960 . A ATG 226.77 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.40;SOR=4.174 GT:AD:DP:GQ:PL 1/1:0,7:7:21:264,21,0 +chr19 39179002 . T C 31.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=15.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0 +chr19 47271315 . C T 513.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.932;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.69;ReadPosRankSum=-1.045;SOR=0.264 GT:AD:DP:GQ:PL 1/1:1,19:20:30:542,30,0 +chr19 47271515 . T C 336.77 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.06;SOR=2.670 GT:AD:DP:GQ:PL 1/1:0,12:12:36:365,36,0 +chr19 47272198 . G T 21.77 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 +chr20 46687147 . C T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.260;DP=26;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.30;ReadPosRankSum=1.395;SOR=1.179 GT:AD:DP:GQ:PL 0/1:8,18:26:99:452,0,165
Binary file ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations-7cf8f5889a4d/tool-data/cravat_tissues.loc.sample Wed Nov 14 12:20:23 2018 -0500 @@ -0,0 +1,27 @@ +Bladder Bladder Urothelial Carcinoma BLCA (TCGA) Jun 2013 +Blood-Lymphocyte Chronic Lymphocytic Leukemia CLL (ICGC) Mar 2013 +Blood-Myeloid Acute Myeloid Leukemia LAML (TCGA) Jun 2013 +Brain-Cerebellum Medulloblastoma MB (mixed source) Dec 2010 +Brain-Glioblastoma-Multiforme Glioblastoma Multiforme GBM (TCGA) Jun 2013 +Brain-Lower-Grade-Glioma Brain Lower Grade Glioma LGG (TCGA) Jun 2013 +Breast Breast Invasive Carcinoma BRCA (TCGA) Jun 12012 +Cervix Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC (TCGA) Jun 2013 +Colon Colon Adenocarcinoma COAD (TCGA) Jun 2013 +Head and Neck Head and Neck Squamous Cell Carcinoma HNSC (TCGA) Jun 2013 +Kidney-Chromophobe Kidney Chromophobe KICH (TCGA) Jun 2013 +Kidney-Clear-Cell Kidney Renal Clear Cell Carcinoma KIRC (TCGA) Jun 2013 +Kidney-Papillary-Cell Kidney Renal Papillary Cell Carcinoma KIRP (TCGA) Jun 2013 +Liver-Nonviral Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity) HCCA (ICGC) Mar 2013 +Liver-Viral Hepatocellular Carcinoma (Viral) HCCV (ICGC) Mar 2013 +Lung-Adenocarcinoma Lung Adenocarcinoma LUAD (TCGA) Jun 2013 +Lung-Squamous Cell Lung Squamous Cell Carcinoma LUSC (TCGA) Jun 2013 +Melanoma Melanoma ML (Yardena Samuels lab) Dec 2011 +Other General purpose OV (TCGA) Jun 2013 +Ovary Ovarian Serous Cystadenocarcinoma OV (TCGA) Jun 2013 +Pancreas Pancreatic Cancer PNCC (ICGC)) Mar 2013 +Prostate-Adenocarcinoma Prostate Adenocarcinoma PRAD (TCGA) Jun 2013 +Rectum Rectum Adenocarcinoma READ (TCGA) Jun 2013 +Skin Skin Cutaneous Melanoma SKCM (TCGA) Jun 2013 +Stomach Stomach Adenocarcinoma STAD (TCGA) Jun 2013 +Thyroid Thyroid Carcinoma THCA (TCGA) Jun 2013 +Uterus Uterine Corpus Endometriod Carcinoma UCEC (TCGA) Jun 2013
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations-7cf8f5889a4d/tool-data/ctat_genome_resource_libs.loc.sample Wed Nov 14 12:20:23 2018 -0500 @@ -0,0 +1,15 @@ +# This file lists the locations of CTAT Genome Resource Libraries +# Usually there will only be one library, but it is concievable +# that there could be multiple libraries. +# This file format is as follows +# (white space characters are TAB characters): +# +#<value> <name> <path> +# value is a unique id +# name is the display name +# path is the directory where the genome resource lib files are stored +# +#ctat_genome_resource_libs.loc could look like: +# +#GRCh38_v27_CTAT_lib_Feb092018 CTAT_GenomeResourceLib_GRCh38_v27_CTAT_lib_Feb092018 /path/to/ctat/genome/resource/lib/directory +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations-7cf8f5889a4d/tool_data_table_conf.xml.sample Wed Nov 14 12:20:23 2018 -0500 @@ -0,0 +1,18 @@ +<tables> + <table name="ctat_genome_resource_libs" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_genome_resource_libs.loc" /> + </table> + <table name="cravat_tissues" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/cravat_tissues.loc" /> + </table> + <table name="ctat_centrifuge_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_centrifuge_indexes.loc" /> + </table> + <table name="ctat_lncrna_annotations" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_lncrna_annotations.loc" /> + </table> +</tables>
--- a/ctat_mutations.xml Wed Nov 14 12:15:58 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -<tool id="ctat_mutations" name="ctat_mutations" version="1.0.0" profile="17.05"> - <description>Mutation Pipeline for calling SNPs and variants</description> - <requirements> - <requirement type="package" version="2.0.1">ctat-mutations</requirement> - </requirements> - <command detect_errors="default"> - <![CDATA[ - ctat_mutations \ - --plot \ - --out_dir varcalling.outdir \ - --threads 8 \ - --variant_filtering_mode GATK \ - --left "$left" \ - --right "$right" \ - --genome_lib_dir "${genome_resource_lib.fields.path}" \ - --variant_call_mode GATK \ - --tissue_type "$tissue_type" \ - --email "$cravat_email" - ]]> - </command> - <inputs> - <param format="fastq" name="left" type="data" label="Left/Forward strand reads" help="Left read"/> - <param format="fastq" name="right" type="data" label="Right/Reverse strand reads" help="Right read"/> - <param name="tissue_type" type="select" label="Select a pathology" help="If you don't know, just choose 'General Purpose'"> - <options from_data_table="ctat_cravat_tissues"> - <filter type="sort_by" column="1"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> - <param name="genome_resource_lib" type="select" label="Select a reference genome"> - <options from_data_table="ctat_genome_resource_libs"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - <param name="cravat_email" type="text" label="CRAVAT email" help="CRAVAT registered email id"/> - <section name="adv" title="This service uses the GATK4. GATK4 is licensed by the Broad Institute and is made available to academic users of this service for non-commercial use only. The full text of the license is available here: https://www.broadinstitute.org/gatk/about/license.html. For more information about GATK and full documentation, please visit the GATK website: https://www.broadinstitute.org." expanded="False"> - </section> - </inputs> - <outputs> - <data format="tabular" name="cancertab" label="${tool.name} on ${on_string}: Cancer Tab" from_work_dir="varcalling.outdir/cancer.tab"/> - <data format="vcf" name="cancerVariants" label="${tool.name} on ${on_string}: Cancer VCF" from_work_dir="varcalling.outdir/cancer.vcf"/> - <data format="vcf" name="allVariants" label="${tool.name} on ${on_string}: All Variants VCF" from_work_dir="varcalling.outdir/variants.vcf"/> - <data format="bam" name="bamfile" label="Bam used in haplotype calling" from_work_dir="varcalling.outdir/misc/recalibrated.bam"/> - <data format="txt" name="cravat" label="Annotated (lightly filtered) VCF file" from_work_dir="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/> - </outputs> - <tests> - <test> - <param name="left" value="reads_1.fastq.gz"/> - <param name="right" value="reads_2.fastq.gz"/> - <param name="tissue_type" value="Other"/> - <output name="cancertab" file="varcalling.outdir/cancer.tab" /> - <output name="cancerVariants" file="varcalling.outdir/cancer.vcf" /> - <output name="allVariants" file="varcalling.outdir/variants.vcf" /> - <output name="bamfile" file="varcalling.outdir/misc/recalibrated.bam" /> - <output name="cravat" file="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/> - </test> - </tests> - <help> - -.. class:: warningmark - -Mutation detection in RNA-Seq highlights the GATK Best Practices in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT. - - </help> - <citations> - </citations> -</tool>
--- a/tool_data_table_conf.xml.sample Wed Nov 14 12:15:58 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<tables> - <table name="ctat_genome_resource_libs" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, path</columns> - <file path="tool-data/ctat_genome_resource_libs.loc" /> - </table> - <table name="cravat_tissues" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, path</columns> - <file path="tool-data/cravat_tissues.loc" /> - </table> - <table name="ctat_centrifuge_indexes" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, path</columns> - <file path="tool-data/ctat_centrifuge_indexes.loc" /> - </table> - <table name="ctat_lncrna_annotations" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, path</columns> - <file path="tool-data/ctat_lncrna_annotations.loc" /> - </table> -</tables>