Mercurial > repos > iuc > gemini_query
changeset 2:9dc6c42486a1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
| author | iuc |
|---|---|
| date | Tue, 16 Feb 2016 05:52:47 -0500 |
| parents | e88b4daf650d |
| children | 87e5559c248e |
| files | gemini_macros.xml gemini_query.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, 133 insertions(+), 11 deletions(-) [+] |
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--- a/gemini_macros.xml Tue Dec 29 11:06:19 2015 -0500 +++ b/gemini_macros.xml Tue Feb 16 05:52:47 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/gemini_query.xml Tue Dec 29 11:06:19 2015 -0500 +++ b/gemini_query.xml Tue Feb 16 05:52:47 2016 -0500 @@ -98,13 +98,14 @@ </test> </tests> <help> +<![CDATA[ **What it does** The real power in the GEMINI framework lies in the fact that all of your genetic variants have been stored in a convenient database in the context of a wealth of genome annotations that facilitate variant interpretation. The expressive power of SQL allows one to pose intricate questions of one’s variation data. This tool offers you an easy way to query your variants! http://gemini.readthedocs.org/en/latest/content/querying.html - +]]> </help> <expand macro="citations"/> </tool>
--- a/repository_dependencies.xml Tue Dec 29 11:06:19 2015 -0500 +++ b/repository_dependencies.xml Tue Feb 16 05:52:47 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 05:52:47 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 05:52:47 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 05:52:47 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 05:52:47 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 05:52:47 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 05:52:47 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 11:06:19 2015 -0500 +++ b/tool_dependencies.xml Tue Feb 16 05:52:47 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>