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annotate test-data/vcfaddinfo-input1.vcf @ 2:b9e24dacef7a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:10:48 -0400
parents 9cf4c4cfa456
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9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 ##fileformat=VCFv4.0
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 ##fileDate=20090805
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 ##source=myImputationProgramV3.1
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 ##reference=1000GenomesPilot-NCBI36
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 ##phasing=partial
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo 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">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 ##FILTER=<ID=q10,Description="Quality below 10">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 ##ALT=<ID=CNV,Description="Copy number variable region">
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 20 14370 rs6054257 G A 29 PASS NS=3;AF=0.5;DB;H2 GT:GQ:HQ 0|0:48:51,51 1|0:48:51,51 1/1:43:.,.
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 20 17330 . T A 3 q10 NS=3;AF=0.017 GT:GQ:HQ 0|0:49:58,50 0|1:3:65,3 0/0:41:.,.
9cf4c4cfa456 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfaddinfo commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2