Mercurial > repos > devteam > vcfannotategenotypes

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c6be83b8883d Uploaded
devteam
parents:
diff changeset
1 ##fileformat=VCFv4.0
c6be83b8883d Uploaded
devteam
parents:
diff changeset
2 ##fileDate=20090805
c6be83b8883d Uploaded
devteam
parents:
diff changeset
3 ##source=myImputationProgramV3.1
c6be83b8883d Uploaded
devteam
parents:
diff changeset
4 ##reference=1000GenomesPilot-NCBI36
c6be83b8883d Uploaded
devteam
parents:
diff changeset
5 ##phasing=partial
c6be83b8883d Uploaded
devteam
parents:
diff changeset
6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
8 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
10 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
11 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
12 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
13 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
14 ##FILTER=<ID=q10,Description="Quality below 10">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
15 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
19 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
21 ##ALT=<ID=CNV,Description="Copy number variable region">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
22 ##INFO=<ID=added-genotypes.has_variant,Number=0,Type=Flag,Description="True if added-genotypes has a called alternate among samples under comparison.">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
23 ##FORMAT=<ID=added-genotypes,Number=1,Type=String,Description="Genotype from added-genotypes.">
c6be83b8883d Uploaded
devteam
parents:
diff changeset
24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
4
84959112d9a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
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
84959112d9a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
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
84959112d9a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
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
84959112d9a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
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
84959112d9a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
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
84959112d9a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
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
0
c6be83b8883d Uploaded
devteam
parents:
diff changeset
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
2
c96a7e49150a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
32 20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. ./.:.
4
84959112d9a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents: 2
diff changeset
33 X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0|2