Mercurial > repos > devteam > vcfrandomsample

annotate test-data/vcfrandomsample-test1.vcf @ 3:f7e6495859b9 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/vcfrandomsample commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:58:59 +0000
parents ad12ba1db0e4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
1 ##fileformat=VCFv4.0
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
2 ##fileDate=20090805
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
3 ##source=myImputationProgramV3.1
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
4 ##reference=1000GenomesPilot-NCBI36
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
5 ##phasing=partial
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample 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">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
10 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
11 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
12 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
13 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
14 ##FILTER=<ID=q10,Description="Quality below 10">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
15 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
19 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
21 ##ALT=<ID=CNV,Description="Copy number variable region">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
22 ##sampling="random sampling using vcfrandomsample -p 1 -r 0.2 /space/anton/galaxy-central/database/files/000/dataset_1.dat using random seed 1"
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
24 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
25 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:.,.
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
26 X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2