Mercurial > repos > iuc > gemini_de_novo
changeset 0:285f519dab87 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gemini_de_novo.xml Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,77 @@ +<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> + <description>Identifying potential de novo mutations</description> + <macros> + <import>gemini_macros.xml</import> + <token name="@BINARY@">de_novo</token> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + gemini @BINARY@ + + #if $report.report_selector != 'all': + --columns "${report.columns}" + #end if + + @CMDLN_SQL_FILTER_FILTER_OPTION@ + + #if int($min_kindreds) > 0: + --min-kindreds $min_kindreds + #end if + + #if str($families).strip(): + --families "$families" + #end if + + $lenient + $allow_unaffected + + + -d $d + + #if int($min_gq) > 0: + --min-gq $min_gq + #end if + + #if int($gt_pl_max) > -1: + --gt-pl-max $gt_pl_max + #end if + + + "${ infile }" + > "${ outfile }" +]]> + </command> + <inputs> + <expand macro="infile" /> + <expand macro="column_filter" /> + <expand macro="filter" /> + <expand macro="min_kindreds" /> + <expand macro="family" /> + <expand macro="lenient" /> + <expand macro="unaffected" /> + <expand macro="min_sequence_depth" /> + <expand macro="min_gq" /> + <expand macro="gt_pl_max" /> + </inputs> + <outputs> + <data name="outfile" format="tabular" /> + </outputs> + <tests> + <test> + <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> + <param name="columns" value="gene,ref,alt,impact" /> + <output name="outfile" file="gemini_de_novo_result.tabular" /> + </test> + </tests> + <help> +**What it does** + +Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, +you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring. + + </help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gemini_macros.xml Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,146 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.18.1">gemini</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>gemini --version</version_command> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + + <xml name="annotation_dir"> + <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database"> + <options from_data_table="gemini_databases"> + <filter type="sort_by" column="0" /> + </options> + </param> + </xml> + + <xml name="add_header_column"> + <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" + label="Add a header of column names to the output" help="(--header)"/> + </xml> + + <xml name="radius"> + <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" > + <validator type="in_range" min="0"/> + </param> + </xml> + <xml name="variant_mode"> + <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" + label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/> + </xml> + + <xml name="column_filter"> + <conditional name="report"> + <param name="report_selector" type="select" label="Columns to include in the report" + help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns."> + <option value="all" selected="True">all</option> + <option value="column_filter">User given columns</option> + </param> + <when value="all"/> + <when value="column_filter"> + <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)"> + <option value="gene">gene</option> + <option value="chrom">chrom</option> + <option value="start">start</option> + <option value="end">end</option> + <option value="ref">ref</option> + <option value="alt">alt</option> + <option value="impact">impact</option> + <option value="impact_severity">impact_severity</option> + <option value="max_aaf_all">alternative allele frequency</option> + </param> + </when> + </conditional> + </xml> + + <xml name="filter"> + <conditional name="filter"> + <param name="filter_selector" type="select" label="Apply additional constraints" + help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter."> + <option value="no">No additional constraints</option> + <option value="yes">Apply additional constraints</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="filter" type="text" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)"> + <expand macro="sanitize_query" /> + </param> + </when> + </conditional> + </xml> + + <xml name="sanitize_query"> + <sanitizer invalid_char=""> + <valid initial="string.printable"/> + </sanitizer> + </xml> + + <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@"> + #if str($filter.filter_selector) == 'yes' and $filter.filter: + #import pipes + --filter ${ pipes.quote( str( $filter.filter ) ) or "''" } + #end if + </token> + + <xml name="family"> + <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/> + </xml> + + <xml name="lenient"> + <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/> + </xml> + + <xml name="unaffected"> + <param name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" label="Report candidates that also impact samples labeled as unaffected." help="(--allow-unaffected)"/> + </xml> + + <xml name="min_kindreds"> + <param name="min_kindreds" type="integer" value="1" label="The min. number of kindreds that must have a candidate variant in a gene" help="default: 1 (--min-kindreds)" /> + </xml> + + <xml name="min_sequence_depth"> + <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample" + help="default: 0 (-d)" /> + </xml> + + <xml name="min_gq"> + <param name="min_gq" type="integer" value="0" label="the minimum genotype quality required for each sample in a family" help="default: 0 (--min-gq)"> + <validator type="in_range" min="0"/> + </param> + </xml> + + <xml name="gt_pl_max"> + <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" /> + </xml> + <token name="@VERSION@">0.18.1</token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003153</citation> + <yield /> + </citations> + </xml> + + <xml name="infile"> + <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." > + <options options_filter_attribute="metadata.gemini_version" > + <filter type="add_value" value="@VERSION@" /> + </options> + <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator> + </param> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,65 @@ +========================= +Galaxy wrapper for GEMINI +========================= + + +GEMINI: a flexible framework for exploring genome variation + +GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of +the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes, +and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very +powerful system for exploring genetic variation for for disease and population genetics. + +Using the GEMINI framework begins by loading a VCF file into a database. Each variant is automatically +annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, +OMIM, dbSNP, KEGG, and HPRD. All of this information is stored in portable SQLite database that allows +one to explore and interpret both coding and non-coding variation using “off-the-shelf” tools or an +enhanced SQL engine. + +Please also see the original [manuscript](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153). + + +============ +Installation +============ + +It is recommended to install this wrapper via the `Galaxy Tool Shed`. + +.. _`Galaxy Tool Shed`: https://testtoolshed.g2.bx.psu.edu/view/iuc/gemini + + +======= +History +======= +- 0.9.1: Initial public release + + +==================== +Detailed description +==================== + +View the original GEMINI documentation: http://gemini.readthedocs.org/en/latest/index.html + + +=============================== +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="This requires the GEMINI data manager definition to install all required annotation databases."> + <repository changeset_revision="345412d58d75" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/anno.bed Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,3 @@ +chr1 30547 30548 +chr1 30920 30925 +chr1 30922 30923
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_actionable_mutations_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,1 @@ +tum_name chrom start end ref alt gene impact is_somatic in_cosmic_census dgidb_info
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_amend_input.ped Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,5 @@ +#family_id name paternal_id maternal_id sex phenotype ethnicity hair_color +1 M10475 None None 1 1 None brown +1 M10478 M10475 M10500 2 2 None red +1 M10500 None None 2 2 None +1 M128215 M10475 M10500 1 1 None green
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_annotate_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,1 @@ +updated 10 variants
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_autosomal_dominant_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,9 @@ +gene chrom impact variant_id family_id family_members family_genotypes samples family_count +ASAH2C chr10 missense_variant 3 3 3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected) C/T,C/C,C/T 3_dad,3_kid 2 +ASAH2C chr10 missense_variant 3 2 2_dad(2_dad;unaffected),2_mom(2_mom;affected),2_kid(2_kid;affected) C/C,C/T,C/T 2_mom,2_kid 2 +ASAH2C chr10 missense_variant 4 3 3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected) C/T,C/C,C/T 3_dad,3_kid 2 +ASAH2C chr10 missense_variant 4 2 2_dad(2_dad;unaffected),2_mom(2_mom;affected),2_kid(2_kid;affected) C/C,C/T,C/T 2_mom,2_kid 2 +SPRN chr10 intron_variant 5 3 3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected) G/A,G/G,G/A 3_dad,3_kid 1 +WDR37 chr10 stop_lost 1 3 3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected) T/C,T/T,T/C 3_dad,3_kid 2 +WDR37 chr10 stop_lost 1 2 2_dad(2_dad;unaffected),2_mom(2_mom;affected),2_kid(2_kid;affected) T/T,T/C,T/C 2_mom,2_kid 2 +WDR37 chr10 stop_lost 2 3 3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected) T/C,T/C,T/C 3_dad,3_kid 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_autosomal_recessive.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,2 @@ +gene chrom impact variant_id family_id family_members family_genotypes samples family_count +WDR37 chr10 stop_lost 2 1 1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected) T/C,T/C,C/C 1_kid 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_burden_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,6 @@ +gene T c Z p_value +SYCE1 -0.5 0.25 -1.0 0.00699300699301 +DHODH 0.0 0.0 nan nan +WDR37 -1.0 1.5 -0.816496580928 0.00699300699301 +ASAH2C -0.5 0.75 -0.57735026919 0.00699300699301 +CTBP2 0.0 0.0 nan nan
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_comphets_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,3 @@ +chrom start end ref alt gene impact variant_id family_id family_members family_genotypes samples family_count comp_het_id priority +chr1 17362 17366 TTCT T WASH7P splice_acceptor_variant 3 4 child_4(child_4;affected;male),dad_4(dad_4;unaffected;male),mom_4(mom_4;unaffected;female) TTCT|T,TTCT/T,TTCT/TTCT child_4 1 1_3_7 3 +chr1 17729 17730 C A WASH7P splice_acceptor_variant 7 4 child_4(child_4;affected;male),dad_4(dad_4;unaffected;male),mom_4(mom_4;unaffected;female) C/A,C/A,C/A child_4 1 1_3_7 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_dbinfo_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,209 @@ +table_name column_name type +variants chrom text +variants start integer +variants end integer +variants vcf_id text +variants variant_id integer +variants anno_id integer +variants ref text +variants alt text +variants qual float +variants filter text +variants type text +variants sub_type text +variants gts blob +variants gt_types blob +variants gt_phases blob +variants gt_depths blob +variants gt_ref_depths blob +variants gt_alt_depths blob +variants gt_quals blob +variants gt_copy_numbers blob +variants gt_phred_ll_homref blob +variants gt_phred_ll_het blob +variants gt_phred_ll_homalt blob +variants call_rate float +variants in_dbsnp bool +variants rs_ids text +variants sv_cipos_start_left integer +variants sv_cipos_end_left integer +variants sv_cipos_start_right integer +variants sv_cipos_end_right integer +variants sv_length integer +variants sv_is_precise bool +variants sv_tool text +variants sv_evidence_type text +variants sv_event_id text +variants sv_mate_id text +variants sv_strand text +variants in_omim bool +variants clinvar_sig text +variants clinvar_disease_name text +variants clinvar_dbsource text +variants clinvar_dbsource_id text +variants clinvar_origin text +variants clinvar_dsdb text +variants clinvar_dsdbid text +variants clinvar_disease_acc text +variants clinvar_in_locus_spec_db bool +variants clinvar_on_diag_assay bool +variants clinvar_causal_allele text +variants pfam_domain text +variants cyto_band text +variants rmsk text +variants in_cpg_island bool +variants in_segdup bool +variants is_conserved bool +variants gerp_bp_score float +variants gerp_element_pval float +variants num_hom_ref integer +variants num_het integer +variants num_hom_alt integer +variants num_unknown integer +variants aaf real +variants hwe decimal(2,7) +variants inbreeding_coeff decimal(2,7) +variants pi decimal(2,7) +variants recomb_rate decimal(2,7) +variants gene text +variants transcript text +variants is_exonic bool +variants is_coding bool +variants is_splicing bool +variants is_lof bool +variants exon text +variants codon_change text +variants aa_change text +variants aa_length text +variants biotype text +variants impact text +variants impact_so text +variants impact_severity text +variants polyphen_pred text +variants polyphen_score float +variants sift_pred text +variants sift_score float +variants anc_allele text +variants rms_bq float +variants cigar text +variants depth integer +variants strand_bias float +variants rms_map_qual float +variants in_hom_run integer +variants num_mapq_zero integer +variants num_alleles integer +variants num_reads_w_dels float +variants haplotype_score float +variants qual_depth float +variants allele_count integer +variants allele_bal float +variants in_hm2 bool +variants in_hm3 bool +variants is_somatic bool +variants somatic_score float +variants in_esp bool +variants aaf_esp_ea decimal(2,7) +variants aaf_esp_aa decimal(2,7) +variants aaf_esp_all decimal(2,7) +variants exome_chip bool +variants in_1kg bool +variants aaf_1kg_amr decimal(2,7) +variants aaf_1kg_eas decimal(2,7) +variants aaf_1kg_sas decimal(2,7) +variants aaf_1kg_afr decimal(2,7) +variants aaf_1kg_eur decimal(2,7) +variants aaf_1kg_all decimal(2,7) +variants grc text +variants gms_illumina float +variants gms_solid float +variants gms_iontorrent float +variants in_cse bool +variants encode_tfbs text +variants encode_dnaseI_cell_count integer +variants encode_dnaseI_cell_list text +variants encode_consensus_gm12878 text +variants encode_consensus_h1hesc text +variants encode_consensus_helas3 text +variants encode_consensus_hepg2 text +variants encode_consensus_huvec text +variants encode_consensus_k562 text +variants vista_enhancers text +variants cosmic_ids text +variants info blob +variants cadd_raw float +variants cadd_scaled float +variants fitcons float +variants in_exac bool +variants aaf_exac_all decimal(2,7) +variants aaf_adj_exac_all decimal(2,7) +variants aaf_adj_exac_afr decimal(2,7) +variants aaf_adj_exac_amr decimal(2,7) +variants aaf_adj_exac_eas decimal(2,7) +variants aaf_adj_exac_fin decimal(2,7) +variants aaf_adj_exac_nfe decimal(2,7) +variants aaf_adj_exac_oth decimal(2,7) +variants aaf_adj_exac_sas decimal(2,7) +variants exac_num_het int +variants exac_num_hom_alt int +variants exac_num_chroms int +variants max_aaf_all REAL +variant_impacts variant_id integer +variant_impacts anno_id integer +variant_impacts gene text +variant_impacts transcript text +variant_impacts is_exonic bool +variant_impacts is_coding bool +variant_impacts is_splicing bool +variant_impacts is_lof bool +variant_impacts exon text +variant_impacts codon_change text +variant_impacts aa_change text +variant_impacts aa_length text +variant_impacts biotype text +variant_impacts impact text +variant_impacts impact_so text +variant_impacts impact_severity text +variant_impacts polyphen_pred text +variant_impacts polyphen_score float +variant_impacts sift_pred text +variant_impacts sift_score float +samples sample_id integer +samples family_id text +samples name text +samples paternal_id text +samples maternal_id text +samples sex text +samples phenotype text +samples ethnicity text +gene_detailed uid integer +gene_detailed chrom text +gene_detailed gene text +gene_detailed is_hgnc bool +gene_detailed ensembl_gene_id text +gene_detailed transcript text +gene_detailed biotype text +gene_detailed transcript_status text +gene_detailed ccds_id text +gene_detailed hgnc_id text +gene_detailed entrez_id text +gene_detailed cds_length text +gene_detailed protein_length text +gene_detailed transcript_start text +gene_detailed transcript_end text +gene_detailed strand text +gene_detailed synonym text +gene_detailed rvis_pct float +gene_detailed mam_phenotype_id text +gene_summary uid integer +gene_summary chrom text +gene_summary gene text +gene_summary is_hgnc bool +gene_summary ensembl_gene_id text +gene_summary hgnc_id text +gene_summary transcript_min_start text +gene_summary transcript_max_end text +gene_summary strand text +gene_summary synonym text +gene_summary rvis_pct float +gene_summary mam_phenotype_id text +gene_summary in_cosmic_census bool
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_de_novo_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,9 @@ +chrom start end vcf_id variant_id anno_id ref alt qual filter type sub_type call_rate in_dbsnp rs_ids sv_cipos_start_left sv_cipos_end_left sv_cipos_start_right sv_cipos_end_right sv_length sv_is_precise sv_tool sv_evidence_type sv_event_id sv_mate_id sv_strand in_omim clinvar_sig clinvar_disease_name clinvar_dbsource clinvar_dbsource_id clinvar_origin clinvar_dsdb clinvar_dsdbid clinvar_disease_acc clinvar_in_locus_spec_db clinvar_on_diag_assay clinvar_causal_allele pfam_domain cyto_band rmsk in_cpg_island in_segdup is_conserved gerp_bp_score gerp_element_pval num_hom_ref num_het num_hom_alt num_unknown aaf hwe inbreeding_coeff pi recomb_rate gene transcript is_exonic is_coding is_splicing is_lof exon codon_change aa_change aa_length biotype impact impact_so impact_severity polyphen_pred polyphen_score sift_pred sift_score anc_allele rms_bq cigar depth strand_bias rms_map_qual in_hom_run num_mapq_zero num_alleles num_reads_w_dels haplotype_score qual_depth allele_count allele_bal in_hm2 in_hm3 is_somatic somatic_score in_esp aaf_esp_ea aaf_esp_aa aaf_esp_all exome_chip in_1kg aaf_1kg_amr aaf_1kg_eas aaf_1kg_sas aaf_1kg_afr aaf_1kg_eur aaf_1kg_all grc gms_illumina gms_solid gms_iontorrent in_cse encode_tfbs encode_dnaseI_cell_count encode_dnaseI_cell_list encode_consensus_gm12878 encode_consensus_h1hesc encode_consensus_helas3 encode_consensus_hepg2 encode_consensus_huvec encode_consensus_k562 vista_enhancers cosmic_ids info cadd_raw cadd_scaled fitcons in_exac aaf_exac_all aaf_adj_exac_all aaf_adj_exac_afr aaf_adj_exac_amr aaf_adj_exac_eas aaf_adj_exac_fin aaf_adj_exac_nfe aaf_adj_exac_oth aaf_adj_exac_sas exac_num_het exac_num_hom_alt exac_num_chroms max_aaf_all gts gt_types gt_phases gt_depths gt_ref_depths gt_alt_depths gt_quals gt_copy_numbers gt_phred_ll_homref gt_phred_ll_het gt_phred_ll_homalt family_id family_members family_genotypes samples family_count +chr10 48003991 48003992 None 2 1 C T 1047.86999512 None snp ts 1.0 1 rs142685947,rs3739968 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q11.22 None 0 1 1 None 3.10871e-42 2 6 1 0 0.444444444444 0.29371811258 -0.35 0.522875816993 1.718591 ASAH2C ENST00000420079 1 1 0 0 exon_10_48003968_48004056 tGt/tAt C540Y 610 protein_coding missense_variant missense_variant MED None None None None None None None 165 None 20.9400005341 0 0 8 0.0 4.382999897 9.52999973297 4 None None None None None 0 None None None 0 1 0.3112 0.4573 0.3855 0.1241 0.5149 0.346645 grc_fix 73.3 40.3 92.8 0 None None None R R R R R R None None None None None 0.553676 1 0.443 0.448537771896 0.288974151858 0.281426746944 0.543088975937 0.524984286612 0.478147713207 0.463529411765 0.418641164716 17495 15317 107302 0.543088975937 ['C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T' 'C/T' 'C/T' 'C/T'] [1 1 3 0 0 1 1 1 1] [False False False False False False False False False] [38 29 23 38 29 23 38 29 23] [1 0 0 1 0 0 1 0 0] [37 29 23 37 29 23 37 29 23] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 2 2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected) C/C,C/C,C/T 2_kid 2 +chr10 48004991 48004992 None 3 1 C T 1047.86999512 None snp ts 1.0 0 None None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q11.22 None 0 1 0 None None 2 6 1 0 0.444444444444 0.29371811258 -0.35 0.522875816993 1.718591 ASAH2C ENST00000420079 1 1 0 0 exon_10_48003968_48004056 tGt/tAt C540Y 610 protein_coding missense_variant missense_variant MED None None None None None None None 165 None 20.9400005341 0 0 8 0.0 4.382999897 9.52999973297 4 None None None None None 0 None None None 0 0 None None None None None None grc_fix None None None 0 None None None R R R R R R None None None None None 0.061011 0 None None None None None None None None None None None None -1.0 ['C/T' 'C/T' 'C/T' 'C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T'] [1 1 1 1 1 3 0 0 1] [False False False False False False False False False] [38 29 23 38 29 23 38 29 23] [1 0 0 1 0 0 1 0 0] [37 29 23 37 29 23 37 29 23] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 3 3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected) C/C,C/C,C/T 3_kid 2 +chr10 135336655 135336656 None 4 1 G A 38.3400001526 None snp ts 1.0 1 rs6537611 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 0 None None 4 5 0 0 0.277777777778 0.248563248239 -0.384615384615 0.424836601307 0.43264 SPRN ENST00000541506 0 0 0 0 151 protein_coding intron_variant intron_variant LOW None None None None None None None 2 None 37.0 4 0 4 0.0 0.0 19.1700000763 4 None None None None None 0 None None None 0 1 0.9957 1 1 0.9297 1 0.980831 None None None None 0 None None None R R R R unknown R None None None None None 0.056701 0 None None None None None None None None None None None None 1.0 ['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A'] [0 0 1 0 0 1 1 1 1] [False False False False False False False False False] [38 29 24 38 29 24 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 24 37 29 24 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 1 1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected) G/G,G/G,G/A 1_kid 2 +chr10 135336655 135336656 None 4 1 G A 38.3400001526 None snp ts 1.0 1 rs6537611 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 0 None None 4 5 0 0 0.277777777778 0.248563248239 -0.384615384615 0.424836601307 0.43264 SPRN ENST00000541506 0 0 0 0 151 protein_coding intron_variant intron_variant LOW None None None None None None None 2 None 37.0 4 0 4 0.0 0.0 19.1700000763 4 None None None None None 0 None None None 0 1 0.9957 1 1 0.9297 1 0.980831 None None None None 0 None None None R R R R unknown R None None None None None 0.056701 0 None None None None None None None None None None None None 1.0 ['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A'] [0 0 1 0 0 1 1 1 1] [False False False False False False False False False] [38 29 24 38 29 24 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 24 37 29 24 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 2 2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected) G/G,G/G,G/A 2_kid 2 +chr10 135369531 135369532 None 5 6 T C 122.620002747 None snp ts 1.0 1 rs3747881,rs386585367 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 1 None 3.86096e-59 6 3 0 0 0.166666666667 0.548506235587 -0.2 0.294117647059 0.022013 SYCE1 ENST00000368517 1 1 0 0 exon_10_135369485_135369551 aAg/aGg K147R 282 protein_coding missense_variant missense_variant MED None None None None None None None 239 None 36.0200004578 2 0 8 0.0 5.71409988403 2.30999994278 2 None None None None None 1 0.0938372093023 0.163867453473 0.117561125634 1 1 0.1844 0.2698 0.2188 0.1997 0.1093 0.197284 None None None None 0 None None None R R R R R R None None None None None 0.487112 1 0.134 0.134286610119 0.184985563041 0.164938655607 0.256026889198 0.122313048744 0.0919761054243 0.113686534216 0.194096927001 13825 1225 121196 0.2698 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C'] [0 0 1 0 0 1 0 0 1] [False False False False False False False False False] [38 29 22 38 29 21 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 22 37 29 21 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 1 1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected) T/T,T/T,T/C 1_kid 3 +chr10 135369531 135369532 None 5 6 T C 122.620002747 None snp ts 1.0 1 rs3747881,rs386585367 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 1 None 3.86096e-59 6 3 0 0 0.166666666667 0.548506235587 -0.2 0.294117647059 0.022013 SYCE1 ENST00000368517 1 1 0 0 exon_10_135369485_135369551 aAg/aGg K147R 282 protein_coding missense_variant missense_variant MED None None None None None None None 239 None 36.0200004578 2 0 8 0.0 5.71409988403 2.30999994278 2 None None None None None 1 0.0938372093023 0.163867453473 0.117561125634 1 1 0.1844 0.2698 0.2188 0.1997 0.1093 0.197284 None None None None 0 None None None R R R R R R None None None None None 0.487112 1 0.134 0.134286610119 0.184985563041 0.164938655607 0.256026889198 0.122313048744 0.0919761054243 0.113686534216 0.194096927001 13825 1225 121196 0.2698 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C'] [0 0 1 0 0 1 0 0 1] [False False False False False False False False False] [38 29 22 38 29 21 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 22 37 29 21 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 3 3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected) T/T,T/T,T/C 3_kid 3 +chr10 135369531 135369532 None 5 6 T C 122.620002747 None snp ts 1.0 1 rs3747881,rs386585367 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 1 None 3.86096e-59 6 3 0 0 0.166666666667 0.548506235587 -0.2 0.294117647059 0.022013 SYCE1 ENST00000368517 1 1 0 0 exon_10_135369485_135369551 aAg/aGg K147R 282 protein_coding missense_variant missense_variant MED None None None None None None None 239 None 36.0200004578 2 0 8 0.0 5.71409988403 2.30999994278 2 None None None None None 1 0.0938372093023 0.163867453473 0.117561125634 1 1 0.1844 0.2698 0.2188 0.1997 0.1093 0.197284 None None None None 0 None None None R R R R R R None None None None None 0.487112 1 0.134 0.134286610119 0.184985563041 0.164938655607 0.256026889198 0.122313048744 0.0919761054243 0.113686534216 0.194096927001 13825 1225 121196 0.2698 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C'] [0 0 1 0 0 1 0 0 1] [False False False False False False False False False] [38 29 22 38 29 21 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 22 37 29 21 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 2 2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected) T/T,T/T,T/C 2_kid 3 +chr10 1142207 1142208 None 1 4 T C 3404.30004883 None snp ts 1.0 1 rs10794716 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10p15.3 None 0 0 0 None None 7 1 1 0 0.166666666667 0.0718606383197 0.6 0.294117647059 0.200924 WDR37 ENST00000381329 1 1 0 1 exon_10_1142110_1142566 Tga/Cga *250R 249 protein_coding stop_lost stop_lost HIGH None None None None None None None 122 None 36.0 0 0 8 0.0 2.67470002174 27.8999996185 8 None None None None None 1 0.999534883721 0.975034044485 0.991234814701 0 1 0.9942 1 1 0.9561 1 0.98762 None None None None 0 None 2 Osteobl;Progfib T T T T T T None None None None None 0.156188 1 0.997 0.997067786838 0.970305592927 0.998358956642 1 1 0.999595432887 0.998898678414 1 346 60354 121410 1.0 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C'] [0 0 1 0 0 0 0 0 3] [False False False False False False False False False] [38 29 23 38 29 22 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 23 37 29 22 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 1 1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected) T/T,T/T,T/C 1_kid 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_dump_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,97 @@ +chrom start end ref alt type sub_type aaf in_dbsnp gene sample genotype +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 child_1 G/A +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 child_2 G/G +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 dad_2 G/A +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 mom_2 G/G +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 dad_1 G/G +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 mom_1 G/A +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 child_3 G/A +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 dad_3 G/A +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 mom_3 G/A +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 child_4 G/A +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 dad_4 G/A +chr1 16976 16977 G A snp ts 0.375 0 DDX11L1 mom_4 G/A +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 child_1 A/A +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 child_2 A/G +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 dad_2 A/A +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 mom_2 A/G +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 dad_1 A/A +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 mom_1 A/A +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 child_3 A/A +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 dad_3 A/A +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 mom_3 A/G +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 child_4 A/G +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 dad_4 A/A +chr1 17221 17222 A G snp ts 0.166666666667 1 DDX11L1 mom_4 A/A +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P child_1 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P child_2 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P dad_2 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P mom_2 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P dad_1 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P mom_1 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P child_3 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P dad_3 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P mom_3 TTCT/TTCT +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P child_4 TTCT/T +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P dad_4 TTCT/T +chr1 17362 17366 TTCT T indel del 0.0833333333333 0 WASH7P mom_4 TTCT/TTCT +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 child_1 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 child_2 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 dad_2 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 mom_2 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 dad_1 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 mom_1 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 child_3 G/A +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 dad_3 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 mom_3 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 child_4 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 dad_4 G/G +chr1 17562 17563 G A snp ts 0.0416666666667 0 DDX11L1 mom_4 G/G +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 child_1 G/C +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 child_2 G/G +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 dad_2 G/G +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 mom_2 G/C +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 dad_1 G/G +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 mom_1 G/G +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 child_3 G/G +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 dad_3 G/C +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 mom_3 G/G +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 child_4 G/C +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 dad_4 G/G +chr1 17696 17697 G C snp tv 0.166666666667 1 DDX11L1 mom_4 G/G +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 child_1 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 child_2 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 dad_2 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 mom_2 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 dad_1 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 mom_1 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 child_3 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 dad_3 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 mom_3 A/A +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 child_4 A/G +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 dad_4 A/G +chr1 17721 17722 A G snp ts 0.125 1 DDX11L1 mom_4 A/G +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P child_1 C/C +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P child_2 C/C +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P dad_2 C/C +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P mom_2 C/C +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P dad_1 C/A +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P mom_1 C/C +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P child_3 C/A +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P dad_3 C/C +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P mom_3 C/C +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P child_4 C/A +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P dad_4 C/A +chr1 17729 17730 C A snp tv 0.208333333333 0 WASH7P mom_4 C/A +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 child_1 A/A +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 child_2 A/A +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 dad_2 A/A +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 mom_2 A/A +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 dad_1 A/G +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 mom_1 A/G +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 child_3 A/G +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 dad_3 A/G +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 mom_3 A/G +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 child_4 A/G +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 dad_4 A/G +chr1 17745 17746 A G snp ts 0.333333333333 1 DDX11L1 mom_4 A/G
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_gene_wise_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,6 @@ +chrom start end gene impact impact_severity max_aaf_all variant_filters n_gene_variants gene_filters +chr10 48003991 48003992 ASAH2C missense_variant MED 0.543088975937 1 1 1 +chr10 126678091 126678092 CTBP2 stop_gained HIGH 0.0904917363803 1 1 1 +chr10 135369531 135369532 SYCE1 missense_variant MED 0.2698 1 1 1 +chr10 1142207 1142208 WDR37 stop_lost HIGH 1.0 1 1 1 +chr16 72057434 72057435 DHODH missense_variant MED 0.000432002764818 1 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_interactions_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,25 @@ +sample gene order_of_interaction interacting_gene +M10475 CTBP2 0_order: none +M10475 CTBP2 1_order: none +M10475 CTBP2 2_order: none +M10475 CTBP2 3_order: none +M10475 CTBP2 4_order: WDR37 +M10475 CTBP2 5_order: none +M128215 CTBP2 0_order: CTBP2 +M128215 CTBP2 1_order: none +M128215 CTBP2 2_order: none +M128215 CTBP2 3_order: none +M128215 CTBP2 4_order: WDR37 +M128215 CTBP2 5_order: none +M10478 CTBP2 0_order: none +M10478 CTBP2 1_order: none +M10478 CTBP2 2_order: none +M10478 CTBP2 3_order: none +M10478 CTBP2 4_order: WDR37 +M10478 CTBP2 5_order: MTG1 +M10500 CTBP2 0_order: none +M10500 CTBP2 1_order: none +M10500 CTBP2 2_order: none +M10500 CTBP2 3_order: none +M10500 CTBP2 4_order: WDR37 +M10500 CTBP2 5_order: MTG1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_load_input.vcf Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,70 @@ +##fileformat=VCFv4.1 +##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD"> +##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder"> +##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder"> +##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder"> +##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints"> +##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints"> +##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count"> +##ALT=<ID=DEL,Description="Deletion"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder"> +##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods"> +##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN"> +##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN"> +##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN"> +##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN"> +##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN"> +##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents"> +##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data"> +##reference=GRCh37 +##SnpEffVersion="SnpEff 3.0f (build 2012-08-23), by Pablo Cingolani" +##SnpEffCmd="SnpEff GRCh37.66 -i vcf -o vcf -c /Users/arq5x/src/other/snpEff_3_0/snpEff.config ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' "> +#CHROM POS ID REF ALT QUAL FILTER INFO +1 10583 rs58108140 G A 100.0 PASS AVGPOST=0.7707;RSQ=0.4319;LDAF=0.2327;ERATE=0.0161;AN=2184;VT=SNP;AA=.;THETA=0.0046;AC=314;SNPSOURCE=LOWCOV;AF=0.14;ASN_AF=0.13;AMR_AF=0.17;AFR_AF=0.04;EUR_AF=0.21;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|) +1 10611 rs189107123 C G 100.0 PASS AN=2184;THETA=0.0077;VT=SNP;AA=.;AC=41;ERATE=0.0048;SNPSOURCE=LOWCOV;AVGPOST=0.9330;LDAF=0.0479;RSQ=0.3475;AF=0.02;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|) +1 13302 rs180734498 C T 100.0 PASS THETA=0.0048;AN=2184;AC=249;VT=SNP;AA=.;RSQ=0.6281;LDAF=0.1573;SNPSOURCE=LOWCOV;AVGPOST=0.8895;ERATE=0.0058;AF=0.11;ASN_AF=0.02;AMR_AF=0.08;AFR_AF=0.21;EUR_AF=0.14;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|) +1 13327 rs144762171 G C 100.0 PASS AVGPOST=0.9698;AN=2184;VT=SNP;AA=.;RSQ=0.6482;AC=59;SNPSOURCE=LOWCOV;ERATE=0.0012;LDAF=0.0359;THETA=0.0204;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|) +1 13957 . TC T 28.0 PASS AA=TC;AC=35;AN=2184;VT=INDEL;AVGPOST=0.8711;RSQ=0.2501;LDAF=0.0788;THETA=0.0100;ERATE=0.0065;AF=0.02;ASN_AF=0.01;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|) +1 13980 rs151276478 T C 100.0 PASS AN=2184;AC=45;ERATE=0.0034;THETA=0.0139;RSQ=0.3603;LDAF=0.0525;VT=SNP;AA=.;AVGPOST=0.9221;SNPSOURCE=LOWCOV;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|) +1 30923 rs140337953 G T 100.0 PASS AC=1584;AA=T;AN=2184;RSQ=0.5481;VT=SNP;THETA=0.0162;SNPSOURCE=LOWCOV;ERATE=0.0183;LDAF=0.6576;AVGPOST=0.7335;AF=0.73;ASN_AF=0.89;AMR_AF=0.80;AFR_AF=0.48;EUR_AF=0.73;EFF=DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER||||177|MIR1302-10|antisense|NON_CODING|ENST00000469289|),INTRON(MODIFIER||||236|MIR1302-10|antisense|NON_CODING|ENST00000473358|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|) +1 46402 . C CTGT 31.0 PASS AA=.;RSQ=0.0960;AN=2184;AC=8;VT=INDEL;AVGPOST=0.8325;THETA=0.0121;ERATE=0.0072;LDAF=0.0903;AF=0.0037;ASN_AF=0.0017;AFR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||) +1 47190 . G GA 192.0 PASS AA=G;AVGPOST=0.9041;AN=2184;AC=29;VT=INDEL;LDAF=0.0628;THETA=0.0153;RSQ=0.2883;ERATE=0.0041;AF=0.01;AMR_AF=0.0028;AFR_AF=0.06;EFF=INTERGENIC(MODIFIER|||||||||) +1 51476 rs187298206 T C 100.0 PASS ERATE=0.0021;AA=C;AC=18;AN=2184;VT=SNP;THETA=0.0103;LDAF=0.0157;SNPSOURCE=LOWCOV;AVGPOST=0.9819;RSQ=0.5258;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||) +1 51479 rs116400033 T A 100.0 PASS RSQ=0.7414;AVGPOST=0.9085;AA=T;AN=2184;THETA=0.0131;AC=235;VT=SNP;LDAF=0.1404;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.11;ASN_AF=0.0035;AMR_AF=0.16;AFR_AF=0.03;EUR_AF=0.22;EFF=INTERGENIC(MODIFIER|||||||||) +1 51914 rs190452223 T G 100.0 PASS ERATE=0.0004;AVGPOST=0.9985;THETA=0.0159;AA=T;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4089;LDAF=0.0012;AF=0.0005;ASN_AF=0.0017;EFF=INTERGENIC(MODIFIER|||||||||) +1 51935 rs181754315 C T 100.0 PASS THETA=0.0126;AA=C;AN=2184;RSQ=0.1888;AVGPOST=0.9972;LDAF=0.0015;VT=SNP;AC=0;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0;EFF=INTERGENIC(MODIFIER|||||||||) +1 51954 rs185832753 G C 100.0 PASS LDAF=0.0021;AA=G;AN=2184;RSQ=0.4692;AVGPOST=0.9975;VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0029;ERATE=0.0006;AC=2;AF=0.0009;AMR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||) +1 52058 rs62637813 G C 100.0 PASS AA=C;ERATE=0.0057;AN=2184;AVGPOST=0.9264;VT=SNP;RSQ=0.4882;AC=64;SNPSOURCE=LOWCOV;LDAF=0.0620;THETA=0.0069;AF=0.03;ASN_AF=0.0017;AMR_AF=0.04;AFR_AF=0.02;EUR_AF=0.05;EFF=INTERGENIC(MODIFIER|||||||||) +1 52144 rs190291950 T A 100.0 PASS THETA=0.0093;ERATE=0.0013;LDAF=0.0156;AA=T;AN=2184;VT=SNP;RSQ=0.5220;AVGPOST=0.9811;SNPSOURCE=LOWCOV;AC=21;AF=0.01;ASN_AF=0.0035;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||) +1 52185 . TTAA T 244.0 PASS AA=.;AN=2184;LDAF=0.0124;VT=INDEL;AC=10;THETA=0.0232;RSQ=0.4271;AVGPOST=0.9840;ERATE=0.0037;AF=0.0046;ASN_AF=0.0035;AMR_AF=0.02;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||) +1 52238 rs150021059 T G 100.0 PASS THETA=0.0132;AA=G;AN=2184;RSQ=0.6256;VT=SNP;ERATE=0.0026;AVGPOST=0.8617;SNPSOURCE=LOWCOV;AC=1941;LDAF=0.8423;AF=0.89;ASN_AF=0.99;AMR_AF=0.93;AFR_AF=0.64;EUR_AF=0.95;EFF=INTERGENIC(MODIFIER|||||||||) +1 53234 . CAT C 227.0 PASS AA=CAT;AVGPOST=0.9936;AN=2184;VT=INDEL;THETA=0.0119;AC=10;LDAF=0.0074;RSQ=0.6237;ERATE=0.0007;AF=0.0046;AMR_AF=0.0028;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||) +1 54353 rs140052487 C A 100.0 PASS THETA=0.0026;AA=C;AN=2184;AC=16;VT=SNP;RSQ=0.5074;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0146;ERATE=0.0058;AF=0.01;ASN_AF=0.01;AMR_AF=0.0028;AFR_AF=0.02;EUR_AF=0.0013;EFF=INTERGENIC(MODIFIER|||||||||) +1 54421 rs146477069 A G 100.0 PASS ERATE=0.0013;AN=2184;AC=220;VT=SNP;RSQ=0.7869;AVGPOST=0.9461;AA=A;THETA=0.0025;SNPSOURCE=LOWCOV;LDAF=0.1190;AF=0.10;ASN_AF=0.25;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||) +1 54490 rs141149254 G A 100.0 PASS ERATE=0.0004;THETA=0.0074;AA=G;AN=2184;VT=SNP;RSQ=0.8366;AVGPOST=0.9646;AC=175;SNPSOURCE=LOWCOV;LDAF=0.0929;AF=0.08;ASN_AF=0.0035;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.15;EFF=INTERGENIC(MODIFIER|||||||||) +1 54676 rs2462492 C T 100.0 PASS LDAF=0.1528;RSQ=0.6989;AA=T;AN=2184;AC=267;VT=SNP;AVGPOST=0.8998;SNPSOURCE=LOWCOV;THETA=0.0110;ERATE=0.0037;AF=0.12;ASN_AF=0.02;AMR_AF=0.20;AFR_AF=0.09;EUR_AF=0.18;EFF=INTERGENIC(MODIFIER|||||||||) +1 54753 rs143174675 T G 100.0 PASS AA=T;AN=2184;RSQ=0.6820;AC=65;VT=SNP;THETA=0.0080;ERATE=0.0016;SNPSOURCE=LOWCOV;AVGPOST=0.9697;LDAF=0.0399;AF=0.03;AMR_AF=0.04;AFR_AF=0.07;EUR_AF=0.03;EFF=INTERGENIC(MODIFIER|||||||||) +1 55164 rs3091274 C A 100.0 PASS AN=2184;VT=SNP;ERATE=0.0045;AA=A;THETA=0.0162;SNPSOURCE=LOWCOV;AC=1955;RSQ=0.6373;AVGPOST=0.8686;LDAF=0.8489;AF=0.90;ASN_AF=0.99;AMR_AF=0.94;AFR_AF=0.65;EUR_AF=0.96;EFF=INTERGENIC(MODIFIER|||||||||) +1 55249 . C CTATGG 443.0 PASS AA=C;AVGPOST=0.9073;ERATE=0.0063;RSQ=0.5891;AN=2184;THETA=0.0038;VT=INDEL;AC=151;LDAF=0.0968;AF=0.07;ASN_AF=0.16;AMR_AF=0.08;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||) +1 55299 rs10399749 C T 100.0 PASS RSQ=0.7602;LDAF=0.2954;AN=2184;VT=SNP;ERATE=0.0051;AA=c;AC=554;SNPSOURCE=LOWCOV;AVGPOST=0.8845;THETA=0.0070;AF=0.25;ASN_AF=0.33;AMR_AF=0.21;AFR_AF=0.39;EUR_AF=0.13;EFF=INTERGENIC(MODIFIER|||||||||) +1 55313 rs182462964 A T 100.0 PASS ERATE=0.0004;RSQ=0.6112;AVGPOST=0.9994;AN=2184;VT=SNP;THETA=0.0057;AA=A;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||) +1 55326 rs3107975 T C 100.0 PASS AA=C;ERATE=0.0074;AN=2184;THETA=0.0085;VT=SNP;SNPSOURCE=LOWCOV;AVGPOST=0.9622;AC=90;RSQ=0.6901;LDAF=0.0562;AF=0.04;ASN_AF=0.07;AMR_AF=0.02;AFR_AF=0.07;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||) +1 55330 rs185215913 G A 100.0 PASS ERATE=0.0005;AA=G;AN=2184;VT=SNP;THETA=0.0086;AVGPOST=0.9988;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4701;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||) +1 55367 rs190850374 G A 100.0 PASS ERATE=0.0004;THETA=0.0044;AA=G;AN=2184;VT=SNP;LDAF=0.0029;RSQ=0.3860;SNPSOURCE=LOWCOV;AVGPOST=0.9961;AC=2;AF=0.0009;AMR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||) +1 55388 rs182711216 C T 100.0 PASS THETA=0.0102;ERATE=0.0005;AA=C;AVGPOST=0.9983;AN=2184;LDAF=0.0010;VT=SNP;RSQ=0.2348;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017;EFF=INTERGENIC(MODIFIER|||||||||) +1 55394 rs2949420 T A 100.0 PASS AC=18;AN=2184;VT=SNP;AA=A;RSQ=0.4995;AVGPOST=0.9784;LDAF=0.0171;SNPSOURCE=LOWCOV;ERATE=0.0012;THETA=0.0063;AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||) +1 55416 rs193242050 G A 100.0 PASS AA=G;AN=2184;AVGPOST=0.9944;VT=SNP;LDAF=0.0064;AC=9;THETA=0.0019;RSQ=0.6553;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0041;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||) +1 55427 rs183189405 T C 100.0 PASS THETA=0.0054;AA=T;AN=2184;VT=SNP;AVGPOST=0.9969;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;RSQ=0.2759;ERATE=0.0007;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||) +1 55816 rs187434873 G A 100.0 PASS AN=2184;THETA=0.0119;VT=SNP;AC=10;RSQ=0.4578;AA=A;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0108;ERATE=0.0007;AF=0.0046;AMR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||) +1 55850 rs191890754 C G 100.0 PASS AVGPOST=0.9921;AA=G;AN=2184;VT=SNP;RSQ=0.4083;THETA=0.0045;LDAF=0.0056;AC=5;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0023;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||) +1 55852 rs184233019 G C 100.0 PASS THETA=0.0137;AA=G;AN=2184;RSQ=0.5433;ERATE=0.0009;LDAF=0.0046;VT=SNP;AVGPOST=0.9953;AC=5;SNPSOURCE=LOWCOV;AF=0.0023;AMR_AF=0.01;EUR_AF=0.0013;EFF=INTERGENIC(MODIFIER|||||||||)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_lofsieve_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,11 @@ +chrom start end ref alt highest_impact aa_change var_trans_pos trans_aa_length var_trans_pct sample genotype gene transcript trans_type +chr10 1142207 1142208 T C stop_lost */R 250 250/249 1.00401606426 M10475 C/C WDR37 ENST00000381329 protein_coding +chr10 1142207 1142208 T C stop_lost */R 250 250/249 1.00401606426 M10478 C/C WDR37 ENST00000381329 protein_coding +chr10 1142207 1142208 T C stop_lost */R 250 250/249 1.00401606426 M10500 C/C WDR37 ENST00000381329 protein_coding +chr10 1142207 1142208 T C stop_lost */R 250 250/249 1.00401606426 M128215 C/C WDR37 ENST00000381329 protein_coding +chr10 126678091 126678092 G A stop_gained Q/* 445 445/445 1.0 M128215 G/A CTBP2 ENST00000531469 protein_coding +chr10 126678091 126678092 G A stop_gained Q/* 445 445/445 1.0 M128215 G/A CTBP2 ENST00000309035 protein_coding +chr10 126678091 126678092 G A stop_gained Q/* 445 445/445 1.0 M128215 G/A CTBP2 ENST00000494626 protein_coding +chr10 126678091 126678092 G A stop_gained Q/* 445 445/445 1.0 M128215 G/A CTBP2 ENST00000337195 protein_coding +chr10 126678091 126678092 G A stop_gained Q/* 445 445/445 1.0 M128215 G/A CTBP2 ENST00000334808 protein_coding +chr10 126678091 126678092 G A stop_gained Q/* 445 445/445 1.0 M128215 G/A CTBP2 ENST00000411419 protein_coding
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_mendel_errors_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,10 @@ +chrom start end vcf_id variant_id anno_id ref alt qual filter type sub_type call_rate in_dbsnp rs_ids sv_cipos_start_left sv_cipos_end_left sv_cipos_start_right sv_cipos_end_right sv_length sv_is_precise sv_tool sv_evidence_type sv_event_id sv_mate_id sv_strand in_omim clinvar_sig clinvar_disease_name clinvar_dbsource clinvar_dbsource_id clinvar_origin clinvar_dsdb clinvar_dsdbid clinvar_disease_acc clinvar_in_locus_spec_db clinvar_on_diag_assay clinvar_causal_allele pfam_domain cyto_band rmsk in_cpg_island in_segdup is_conserved gerp_bp_score gerp_element_pval num_hom_ref num_het num_hom_alt num_unknown aaf hwe inbreeding_coeff pi recomb_rate gene transcript is_exonic is_coding is_splicing is_lof exon codon_change aa_change aa_length biotype impact impact_so impact_severity polyphen_pred polyphen_score sift_pred sift_score anc_allele rms_bq cigar depth strand_bias rms_map_qual in_hom_run num_mapq_zero num_alleles num_reads_w_dels haplotype_score qual_depth allele_count allele_bal in_hm2 in_hm3 is_somatic somatic_score in_esp aaf_esp_ea aaf_esp_aa aaf_esp_all exome_chip in_1kg aaf_1kg_amr aaf_1kg_eas aaf_1kg_sas aaf_1kg_afr aaf_1kg_eur aaf_1kg_all grc gms_illumina gms_solid gms_iontorrent in_cse encode_tfbs encode_dnaseI_cell_count encode_dnaseI_cell_list encode_consensus_gm12878 encode_consensus_h1hesc encode_consensus_helas3 encode_consensus_hepg2 encode_consensus_huvec encode_consensus_k562 vista_enhancers cosmic_ids info cadd_raw cadd_scaled fitcons in_exac aaf_exac_all aaf_adj_exac_all aaf_adj_exac_afr aaf_adj_exac_amr aaf_adj_exac_eas aaf_adj_exac_fin aaf_adj_exac_nfe aaf_adj_exac_oth aaf_adj_exac_sas exac_num_het exac_num_hom_alt exac_num_chroms max_aaf_all gts gt_types gt_phases gt_depths gt_ref_depths gt_alt_depths gt_quals gt_copy_numbers gt_phred_ll_homref gt_phred_ll_het gt_phred_ll_homalt family_id family_members family_genotypes samples family_count violation violation_prob +chr10 1142207 1142208 None 1 4 T C 3404.30004883 None snp ts 1.0 1 rs10794716 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10p15.3 None 0 0 0 None None 7 1 1 0 0.166666666667 0.0718606383197 0.6 0.294117647059 0.200924 WDR37 ENST00000381329 1 1 0 1 exon_10_1142110_1142566 Tga/Cga *250R 249 protein_coding stop_lost stop_lost HIGH None None None None None None None 122 None 36.0 0 0 8 0.0 2.67470002174 27.8999996185 8 None None None None None 1 0.999534883721 0.975034044485 0.991234814701 0 1 0.9942 1 1 0.9561 1 0.98762 None None None None 0 None 2 Osteobl;Progfib T T T T T T None None None None None 0.156188 1 0.997 0.997067786838 0.970305592927 0.998358956642 1 1 0.999595432887 0.998898678414 1 346 60354 121410 1.0 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C'] [0 0 1 0 0 0 0 0 3] [False False False False False False False False False] [38 29 23 38 29 22 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 23 37 29 22 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 1 1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected) T/T,T/T,T/C 1_kid 2 plausible de novo;implausible de novo 0.00000 +chr10 1142207 1142208 None 1 4 T C 3404.30004883 None snp ts 1.0 1 rs10794716 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10p15.3 None 0 0 0 None None 7 1 1 0 0.166666666667 0.0718606383197 0.6 0.294117647059 0.200924 WDR37 ENST00000381329 1 1 0 1 exon_10_1142110_1142566 Tga/Cga *250R 249 protein_coding stop_lost stop_lost HIGH None None None None None None None 122 None 36.0 0 0 8 0.0 2.67470002174 27.8999996185 8 None None None None None 1 0.999534883721 0.975034044485 0.991234814701 0 1 0.9942 1 1 0.9561 1 0.98762 None None None None 0 None 2 Osteobl;Progfib T T T T T T None None None None None 0.156188 1 0.997 0.997067786838 0.970305592927 0.998358956642 1 1 0.999595432887 0.998898678414 1 346 60354 121410 1.0 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C'] [0 0 1 0 0 0 0 0 3] [False False False False False False False False False] [38 29 23 38 29 22 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 23 37 29 22 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 3 3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected) T/T,T/T,C/C 3_kid 2 plausible de novo;implausible de novo 0.00000 +chr10 48003991 48003992 None 2 1 C T 1047.86999512 None snp ts 1.0 1 rs142685947,rs3739968 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q11.22 None 0 1 1 None 3.10871e-42 2 6 1 0 0.444444444444 0.29371811258 -0.35 0.522875816993 1.718591 ASAH2C ENST00000420079 1 1 0 0 exon_10_48003968_48004056 tGt/tAt C540Y 610 protein_coding missense_variant missense_variant MED None None None None None None None 165 None 20.9400005341 0 0 8 0.0 4.382999897 9.52999973297 4 None None None None None 0 None None None 0 1 0.3112 0.4573 0.3855 0.1241 0.5149 0.346645 grc_fix 73.3 40.3 92.8 0 None None None R R R R R R None None None None None 0.553676 1 0.443 0.448537771896 0.288974151858 0.281426746944 0.543088975937 0.524984286612 0.478147713207 0.463529411765 0.418641164716 17495 15317 107302 0.543088975937 ['C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T' 'C/T' 'C/T' 'C/T'] [1 1 3 0 0 1 1 1 1] [False False False False False False False False False] [38 29 23 38 29 23 38 29 23] [1 0 0 1 0 0 1 0 0] [37 29 23 37 29 23 37 29 23] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 2 2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected) C/C,C/C,C/T 2_kid 1 plausible de novo 0.00000 +chr10 48004991 48004992 None 3 1 C T 1047.86999512 None snp ts 1.0 0 None None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q11.22 None 0 1 0 None None 2 6 1 0 0.444444444444 0.29371811258 -0.35 0.522875816993 1.718591 ASAH2C ENST00000420079 1 1 0 0 exon_10_48003968_48004056 tGt/tAt C540Y 610 protein_coding missense_variant missense_variant MED None None None None None None None 165 None 20.9400005341 0 0 8 0.0 4.382999897 9.52999973297 4 None None None None None 0 None None None 0 0 None None None None None None grc_fix None None None 0 None None None R R R R R R None None None None None 0.061011 0 None None None None None None None None None None None None -1.0 ['C/T' 'C/T' 'C/T' 'C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T'] [1 1 1 1 1 3 0 0 1] [False False False False False False False False False] [38 29 23 38 29 23 38 29 23] [1 0 0 1 0 0 1 0 0] [37 29 23 37 29 23 37 29 23] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 3 3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected) C/C,C/C,C/T 3_kid 1 plausible de novo 0.00000 +chr10 135336655 135336656 None 4 1 G A 38.3400001526 None snp ts 1.0 1 rs6537611 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 0 None None 4 5 0 0 0.277777777778 0.248563248239 -0.384615384615 0.424836601307 0.43264 SPRN ENST00000541506 0 0 0 0 151 protein_coding intron_variant intron_variant LOW None None None None None None None 2 None 37.0 4 0 4 0.0 0.0 19.1700000763 4 None None None None None 0 None None None 0 1 0.9957 1 1 0.9297 1 0.980831 None None None None 0 None None None R R R R unknown R None None None None None 0.056701 0 None None None None None None None None None None None None 1.0 ['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A'] [0 0 1 0 0 1 1 1 1] [False False False False False False False False False] [38 29 24 38 29 24 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 24 37 29 24 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 1 1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected) G/G,G/G,G/A 1_kid 2 plausible de novo;plausible de novo 0.00000 +chr10 135336655 135336656 None 4 1 G A 38.3400001526 None snp ts 1.0 1 rs6537611 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 0 None None 4 5 0 0 0.277777777778 0.248563248239 -0.384615384615 0.424836601307 0.43264 SPRN ENST00000541506 0 0 0 0 151 protein_coding intron_variant intron_variant LOW None None None None None None None 2 None 37.0 4 0 4 0.0 0.0 19.1700000763 4 None None None None None 0 None None None 0 1 0.9957 1 1 0.9297 1 0.980831 None None None None 0 None None None R R R R unknown R None None None None None 0.056701 0 None None None None None None None None None None None None 1.0 ['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A'] [0 0 1 0 0 1 1 1 1] [False False False False False False False False False] [38 29 24 38 29 24 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 24 37 29 24 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 2 2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected) G/G,G/G,G/A 2_kid 2 plausible de novo;plausible de novo 0.00000 +chr10 135369531 135369532 None 5 6 T C 122.620002747 None snp ts 1.0 1 rs3747881,rs386585367 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 1 None 3.86096e-59 6 3 0 0 0.166666666667 0.548506235587 -0.2 0.294117647059 0.022013 SYCE1 ENST00000368517 1 1 0 0 exon_10_135369485_135369551 aAg/aGg K147R 282 protein_coding missense_variant missense_variant MED None None None None None None None 239 None 36.0200004578 2 0 8 0.0 5.71409988403 2.30999994278 2 None None None None None 1 0.0938372093023 0.163867453473 0.117561125634 1 1 0.1844 0.2698 0.2188 0.1997 0.1093 0.197284 None None None None 0 None None None R R R R R R None None None None None 0.487112 1 0.134 0.134286610119 0.184985563041 0.164938655607 0.256026889198 0.122313048744 0.0919761054243 0.113686534216 0.194096927001 13825 1225 121196 0.2698 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C'] [0 0 1 0 0 1 0 0 1] [False False False False False False False False False] [38 29 22 38 29 21 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 22 37 29 21 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 1 1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected) T/T,T/T,T/C 1_kid 3 plausible de novo;plausible de novo;plausible de novo 0.00000 +chr10 135369531 135369532 None 5 6 T C 122.620002747 None snp ts 1.0 1 rs3747881,rs386585367 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 1 None 3.86096e-59 6 3 0 0 0.166666666667 0.548506235587 -0.2 0.294117647059 0.022013 SYCE1 ENST00000368517 1 1 0 0 exon_10_135369485_135369551 aAg/aGg K147R 282 protein_coding missense_variant missense_variant MED None None None None None None None 239 None 36.0200004578 2 0 8 0.0 5.71409988403 2.30999994278 2 None None None None None 1 0.0938372093023 0.163867453473 0.117561125634 1 1 0.1844 0.2698 0.2188 0.1997 0.1093 0.197284 None None None None 0 None None None R R R R R R None None None None None 0.487112 1 0.134 0.134286610119 0.184985563041 0.164938655607 0.256026889198 0.122313048744 0.0919761054243 0.113686534216 0.194096927001 13825 1225 121196 0.2698 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C'] [0 0 1 0 0 1 0 0 1] [False False False False False False False False False] [38 29 22 38 29 21 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 22 37 29 21 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 3 3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected) T/T,T/T,T/C 3_kid 3 plausible de novo;plausible de novo;plausible de novo 0.00000 +chr10 135369531 135369532 None 5 6 T C 122.620002747 None snp ts 1.0 1 rs3747881,rs386585367 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q26.3 None 0 0 1 None 3.86096e-59 6 3 0 0 0.166666666667 0.548506235587 -0.2 0.294117647059 0.022013 SYCE1 ENST00000368517 1 1 0 0 exon_10_135369485_135369551 aAg/aGg K147R 282 protein_coding missense_variant missense_variant MED None None None None None None None 239 None 36.0200004578 2 0 8 0.0 5.71409988403 2.30999994278 2 None None None None None 1 0.0938372093023 0.163867453473 0.117561125634 1 1 0.1844 0.2698 0.2188 0.1997 0.1093 0.197284 None None None None 0 None None None R R R R R R None None None None None 0.487112 1 0.134 0.134286610119 0.184985563041 0.164938655607 0.256026889198 0.122313048744 0.0919761054243 0.113686534216 0.194096927001 13825 1225 121196 0.2698 ['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C'] [0 0 1 0 0 1 0 0 1] [False False False False False False False False False] [38 29 22 38 29 21 38 29 24] [1 0 0 1 0 0 1 0 0] [37 29 22 37 29 21 37 29 24] [ 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939 87.16000366 78.19999695 66.13999939] None [940 899 729 940 899 729 940 899 729] [87 78 66 87 78 66 87 78 66] [0 0 0 0 0 0 0 0 0] 2 2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected) T/T,T/T,T/C 2_kid 3 plausible de novo;plausible de novo;plausible de novo 0.00000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_pathways_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,17 @@ +chrom start end ref alt impact sample genotype gene transcript pathway +chr10 52004314 52004315 T C intron_variant M10500 C/C ASAH2 ENST00000329428 hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways +chr10 52004314 52004315 T C intron_variant M128215 C/C ASAH2 ENST00000329428 hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways +chr10 52004314 52004315 T C intron_variant M10500 C/C ASAH2 ENST00000447815 hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways +chr10 52004314 52004315 T C intron_variant M128215 C/C ASAH2 ENST00000447815 hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways +chr10 52004314 52004315 T C intron_variant M10500 C/C ASAH2 ENST00000395526 hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways +chr10 52004314 52004315 T C intron_variant M128215 C/C ASAH2 ENST00000395526 hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways +chr10 126678091 126678092 G A stop_gained M128215 G/A CTBP2 ENST00000531469 hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer +chr10 126678091 126678092 G A stop_gained M128215 G/A CTBP2 ENST00000309035 hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer +chr10 126678091 126678092 G A stop_gained M128215 G/A CTBP2 ENST00000494626 hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer +chr10 126678091 126678092 G A stop_gained M128215 G/A CTBP2 ENST00000337195 hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer +chr10 126678091 126678092 G A stop_gained M128215 G/A CTBP2 ENST00000411419 hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer +chr10 135336655 135336656 G A intron_variant M10478 A/A CYP2E1 ENST00000463117 hsa00982:Drug_metabolism_cytochrome_P450,hsa01100:Metabolic_pathways,hsa00590:Arachidonic_acid_metabolism,hsa00980:Metabolism_of_xenobiotics_by_cytochrome_P450,hsa00591:Linoleic_acid_metabolism +chr10 135336655 135336656 G A intron_variant M128215 A/A CYP2E1 ENST00000463117 hsa00982:Drug_metabolism_cytochrome_P450,hsa01100:Metabolic_pathways,hsa00590:Arachidonic_acid_metabolism,hsa00980:Metabolism_of_xenobiotics_by_cytochrome_P450,hsa00591:Linoleic_acid_metabolism +chr10 135336655 135336656 G A upstream_gene_variant M10478 A/A CYP2E1 ENST00000252945 hsa00982:Drug_metabolism_cytochrome_P450,hsa01100:Metabolic_pathways,hsa00590:Arachidonic_acid_metabolism,hsa00980:Metabolism_of_xenobiotics_by_cytochrome_P450,hsa00591:Linoleic_acid_metabolism +chr10 135336655 135336656 G A upstream_gene_variant M128215 A/A CYP2E1 ENST00000252945 hsa00982:Drug_metabolism_cytochrome_P450,hsa01100:Metabolic_pathways,hsa00590:Arachidonic_acid_metabolism,hsa00980:Metabolism_of_xenobiotics_by_cytochrome_P450,hsa00591:Linoleic_acid_metabolism +chr16 72057434 72057435 C T missense_variant M10475 C/T DHODH ENST00000219240 hsa01100:Metabolic_pathways,hsa00240:Pyrimidine_metabolism
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_qc_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,5 @@ +sample sex chrX_homref chrX_het chrX_homalt chrX_unknown +M10475 male 0 0 0 0 +M10478 female 0 0 0 0 +M10500 female 0 0 0 0 +M128215 male 0 0 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_query_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,10 @@ +10582 +10610 +13301 +13326 +13956 +13979 +30922 +46401 +47189 +51475
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_region_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,1 @@ +chr10 48003991 48003992 None 2 1 C T 1047.86999512 None snp ts 1.0 1 rs142685947,rs3739968 None None None None None 1 None None None None None None None None None None None None None None None None None None chr10q11.22 None 0 1 1 None 3.10871e-42 1 2 1 0 0.5 1 0 0.571428571429 1.718591 ASAH2C ENST00000420079 1 1 0 0 16/17 tGt/tAt C/Y 542/612 protein_coding missense_variant missense_variant MED benign 0.0 tolerated 1.0 None None None 165 None 20.9400005341 0 0 8 0.0 4.382999897 9.52999973297 4 None None None None None 0 None None None 0 1 0.3112 0.4573 0.3855 0.1241 0.5149 0.346645 grc_fix 73.3 40.3 92.8 0 None None None R R R R R R None None None None None 0.553676 1 0.443 0.448537771896 0.288974151858 0.281426746944 0.543088975937 0.524984286612 0.478147713207 0.463529411765 0.418641164716 17495 15317 107302 1 0.543088975937
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_roh_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,7 @@ +chrom start end sample num_of_snps density_per_kb run_length_in_bp +chr10 1142208 135369532 M10475 5 0.0 134227324 +chr10 1142208 135210791 M10500 5 0.0001 134068583 +chr10 1142208 135210791 M10478 5 0.0001 134068583 +chr10 1142208 135336656 M10478 4 0.0 134194448 +chr10 1142208 135336656 M128215 6 0.0001 134194448 +chr10 1142208 135369532 M128215 5 0.0 134227324
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_stats_result.tabular Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,5 @@ +sample total +M10475 3 +M10478 6 +M10500 6 +M128215 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gemini_databases.loc.sample Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,3 @@ +## GEMINI databases +#Version dbkey Description Path +#08_08_2014 hg19 Database (08-08-2014) /path/to/data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,7 @@ +<tables> + <table name="gemini_databases" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gemini_databases.loc" /> + </table> +</tables> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Feb 18 08:57:08 2016 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="gemini" version="0.18.1"> + <repository changeset_revision="be869e11582f" name="package_gemini_0_18_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>