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annotate test-data/vcffilter-test2.vcf @ 10:4bdc111b2470 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit f28d66c0bcad8ac29be2afec28bc639317239775
author iuc
date Tue, 01 Oct 2024 13:48:17 +0000
parents 81972652519c
children
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8
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.0
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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2 ##fileDate=20090805
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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3 ##source=myImputationProgramV3.1
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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4 ##reference=1000GenomesPilot-NCBI36
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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5 ##phasing=partial
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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6 ##filter="!( DP > 10 )"
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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7 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
parents:
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8 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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9 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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10 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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11 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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12 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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13 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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14 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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15 ##FILTER=<ID=q10,Description="Quality below 10">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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16 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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17 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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18 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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19 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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20 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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21 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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22 ##ALT=<ID=CNV,Description="Copy number variable region">
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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24 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:.,.
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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25 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:.,.
81972652519c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
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26 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:.,.