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comparison test-data/vcfannotategenotypes-test1.vcf @ 4:84959112d9a6 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 08:04:28 -0500
parents c96a7e49150a
children
comparison
equal deleted inserted replaced
3:70bc6ced57f7 4:84959112d9a6
20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> 20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
21 ##ALT=<ID=CNV,Description="Copy number variable region"> 21 ##ALT=<ID=CNV,Description="Copy number variable region">
22 ##INFO=<ID=added-genotypes.has_variant,Number=0,Type=Flag,Description="True if added-genotypes has a called alternate among samples under comparison."> 22 ##INFO=<ID=added-genotypes.has_variant,Number=0,Type=Flag,Description="True if added-genotypes has a called alternate among samples under comparison.">
23 ##FORMAT=<ID=added-genotypes,Number=1,Type=String,Description="Genotype from added-genotypes."> 23 ##FORMAT=<ID=added-genotypes,Number=1,Type=String,Description="Genotype from added-genotypes.">
24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
25 19 111 . A C 9.6 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0/0 0|0:10,10:./. 0/1:3,3:0/1 25 19 111 . A C 9.6 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0|0 0|0:10,10:./. 0/1:3,3:0/1
26 19 112 . A G 10 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0/0 0|0:10,10:./. 0/1:3,3:0/1 26 19 112 . A G 10 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0|0 0|0:10,10:./. 0/1:3,3:0/1
27 20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:48:1:51,51:0/0 1|0:48:8:51,51:./. 1/1:43:5:.,.:1/1 27 20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:48:1:51,51:0|0 1|0:48:8:51,51:./. 1/1:43:5:.,.:1/1
28 20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:49:3:58,50:0/0 0|1:3:5:65,3:./. 0/0:41:3:.,.:0/0 28 20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:49:3:58,50:0|0 0|1:3:5:65,3:./. 0/0:41:3:.,.:0/0
29 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 1|2:21:6:23,27:1/2 2|1:2:0:18,2:./. 2/2:35:4:.,.:2/2 29 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 1|2:21:6:23,27:1|2 2|1:2:0:18,2:./. 2/2:35:4:.,.:2/2
30 20 1230237 . T . 47 PASS AA=T;DP=13;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:54:.:56,60:0/0 0|0:48:4:51,51:./. 0/0:61:2:.,.:0/0 30 20 1230237 . T . 47 PASS AA=T;DP=13;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:54:.:56,60:0|0 0|0:48:4:51,51:./. 0/0:61:2:.,.:0/0
31 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant GT:GQ:DP:added-genotypes 0/1:.:4:0/1 0/2:17:2:./. 1/1:40:3:1/1 31 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant GT:GQ:DP:added-genotypes 0/1:.:4:0/1 0/2:17:2:./. 1/1:40:3:1/1
32 20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. ./.:. 32 20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. ./.:.
33 X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0/2 33 X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0|2