Mercurial > repos > iuc > bcftools_view

annotate test-data/filter.1.vcf @ 9:338a2860a20c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
author iuc
date Mon, 29 Jul 2019 17:57:42 -0400
parents 94f98eb08abc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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1 ##fileformat=VCFv4.1
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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3 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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5 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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8 ##FILTER=<ID=q10,Description="Quality below 10">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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9 ##test=<xx=A,yy=B,zz=C>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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10 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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11 ##contig=<ID=1,assembly=b37,length=249250621>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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12 ##contig=<ID=2,assembly=b37,length=249250621>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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13 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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14 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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15 ##readme=AAAAAA
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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16 ##readme=BBBBBB
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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17 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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18 1 1000 . G A 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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19 1 1001 . G A 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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20 1 1003 . GT G 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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21 1 1006 . G A 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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22 1 1007 . G A 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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23 1 2000 . T C 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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24 1 2001 . T C 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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25 1 2003 . T TC 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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26 1 2005 . T C 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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27 1 2006 . T C 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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28 2 1001 . GT G 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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29 2 1004 . GT G 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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30 2 1008 . GT G 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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31 2 2001 . A AT 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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32 2 2003 . A AT 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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33 2 2006 . A AT 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20