Mercurial > repos > devteam > vcfallelicprimitives

annotate test-data/vcfallelicprimitives-test1.vcf @ 3:d5ecdca44759 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/vcfallelicprimitives commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:52:39 +0000
parents c58ebedf1159
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
1 ##fileformat=VCFv4.0
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
2 ##fileDate=20090805
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
3 ##source=myImputationProgramV3.1
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
4 ##reference=1000GenomesPilot-NCBI36
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
5 ##phasing=partial
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
10 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
11 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
12 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
13 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
14 ##FILTER=<ID=q10,Description="Quality below 10">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
15 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
19 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
21 ##ALT=<ID=CNV,Description="Copy number variable region">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
22 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
23 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
24 ##INFO=<ID=Split primitives,Number=0,Type=Flag,Description="The allele was parsed using vcfallelicprimitives.">
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
25 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
26 19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
27 19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
28 20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
29 20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,.
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
30 20 1110696 . A G,T 67 PASS AF=0.333,0.667;LEN=1,1;TYPE=snp,snp;Split primitives GT 1|2 2|1 2|2
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
31 20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
32 20 1234567 . G GA,GAC 50 PASS AC=3,1;LEN=1,2;TYPE=ins,ins;Split primitives GT 0|1 0|2 1|1
1
c58ebedf1159 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
33 20 1235237 . T . 0 . . GT 0/0 0|0 ./.
0
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
34 X 10 . AC ATC,A 10 PASS LEN=1,1;TYPE=ins,del;Split primitives GT 0 0|2 0|1
bbf46057ef48 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
35 X 11 . C G 10 PASS LEN=1;TYPE=snp;Split primitives GT 0 0|0 0|1