Mercurial > repos > iuc > gemini_comp_hets
changeset 2:f52ad3dcee4e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
| author | iuc |
|---|---|
| date | Tue, 16 Feb 2016 05:52:05 -0500 |
| parents | 4c4f5f89cda2 |
| children | ac78943ce161 |
| files | gemini_comp_hets.xml gemini_macros.xml repository_dependencies.xml test-data/gemini_actionable_mutations_result.tabular test-data/gemini_amend_input.db test-data/gemini_amend_input.ped test-data/gemini_amend_result.db test-data/gemini_dump_result.tabular test-data/gemini_fusions_result.tabular test-data/gemini_gene_wise_result.tabular test-data/gemini_is_somatic_result.db test-data/gemini_mendel_errors_result.tabular test-data/gemini_qc_result.tabular tool_dependencies.xml |
| diffstat | 13 files changed, 135 insertions(+), 21 deletions(-) [+] |
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--- a/gemini_comp_hets.xml Tue Dec 29 11:05:46 2015 -0500 +++ b/gemini_comp_hets.xml Tue Feb 16 05:52:05 2016 -0500 @@ -22,7 +22,7 @@ #end if #if str($families).strip(): - --families $families + --families "$families" #end if -d $d @@ -52,18 +52,11 @@ <expand macro="family" /> <expand macro="unaffected" /> <expand macro="min_sequence_depth" /> - <param name="min_genotypequality" 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> - <param name="gt_pl_max" type="integer" value="-1" label="The maximum phred-scaled genotype (PL) allowed for each sample in a family." help="default: -1 not set (--gt-pl-max)"> - <validator type="in_range" min="-1"/> - </param> + <param name="min_genotypequality" type="integer" value="0" min="0" label="The minimum genotype quality required for each sample in a family." help="default: 0 (--min-gq)" /> + <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype (PL) allowed for each sample in a family." help="default: -1 not set (--gt-pl-max)" /> <param name="pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="False" label="Find compound hets by inheritance pattern, without regard to affection" help="(--pattern-only)"/> - <param name="max_priority" type="integer" value="1" label="Default is to show only confident compound hets. Set to 2 or higher to include pairs that are less likely true comp-hets." help="default: 1 (--max-priority)"> - <validator type="in_range" min="1"/> - </param> - + <param name="max_priority" type="integer" value="1" min="1" label="Default is to show only confident compound hets. Set to 2 or higher to include pairs that are less likely true comp-hets." help="default: 1 (--max-priority)" /> </inputs> <outputs> <data name="outfile" format="tabular" />
--- a/gemini_macros.xml Tue Dec 29 11:05:46 2015 -0500 +++ b/gemini_macros.xml Tue Feb 16 05:52:05 2016 -0500 @@ -60,6 +60,7 @@ <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> @@ -111,10 +112,8 @@ </xml> <xml name="min_sequence_depth"> - <param name="d" type="integer" value="0" label="The minimum aligned sequence depth (genotype DP) required for each sample" - help="default: 0 (-d)"> - <validator type="in_range" min="0"/> - </param> + <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"> @@ -124,11 +123,9 @@ </xml> <xml name="gt_pl_max"> - <param name="gt_pl_max" type="integer" value="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)"> - <validator type="in_range" min="-1"/> - </param> + <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@">0.18.0</token> + <token name="@VERSION@">0.18.1</token> <xml name="citations"> <citations>
--- a/repository_dependencies.xml Tue Dec 29 11:05:46 2015 -0500 +++ b/repository_dependencies.xml Tue Feb 16 05:52:05 2016 -0500 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the GEMINI data manager definition to install all required annotation databases."> - <repository changeset_revision="b68b5cd8b58a" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="eb54ffdea8a0" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_actionable_mutations_result.tabular Tue Feb 16 05:52:05 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 Tue Feb 16 05:52:05 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_dump_result.tabular Tue Feb 16 05:52:05 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 Tue Feb 16 05:52:05 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_mendel_errors_result.tabular Tue Feb 16 05:52:05 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_qc_result.tabular Tue Feb 16 05:52:05 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
--- a/tool_dependencies.xml Tue Dec 29 11:05:46 2015 -0500 +++ b/tool_dependencies.xml Tue Feb 16 05:52:05 2016 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="gemini" version="0.18.1"> - <repository changeset_revision="4afa532941cb" name="package_gemini_0_18_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="13ce32ffda3a" name="package_gemini_0_18_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>