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annotate test-data/vcfannotategenotypes-test1.vcf @ 2:7036240872d0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:11:44 -0400
parents 9c9969071728
children 6a3ea8fff5fd
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7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 ##fileformat=VCFv4.0
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 ##fileDate=20090805
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 ##source=myImputationProgramV3.1
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 ##reference=1000GenomesPilot-NCBI36
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 ##phasing=partial
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 ##FILTER=<ID=q10,Description="Quality below 10">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 ##ALT=<ID=CNV,Description="Copy number variable region">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 ##INFO=<ID=added-genotypes.has_variant,Number=0,Type=Flag,Description="True if added-genotypes has a called alternate among samples under comparison.">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 ##FORMAT=<ID=added-genotypes,Number=1,Type=String,Description="Genotype from added-genotypes.">
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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
7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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
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9c9969071728 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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32 20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. ./.:.
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7a32e4b43579 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0/2