Mercurial > repos > iuc > bcftools_filter

annotate test-data/merge.2.b.vcf @ 11:0117c6d2ab96 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
author iuc
date Wed, 25 Dec 2019 12:34:35 -0500
parents 061729be105d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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1 ##fileformat=VCFv4.1
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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3 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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7 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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8 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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9 ##FILTER=<ID=q10,Description="Quality below 10">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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10 ##FILTER=<ID=test,Description="Testing filter">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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11 ##contig=<ID=1,assembly=b37,length=249250621>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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12 ##contig=<ID=2,assembly=b37,length=249250621>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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13 ##contig=<ID=3,assembly=b37,length=198022430>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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14 ##contig=<ID=4,assembly=b37,length=191154276>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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15 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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16 ##readme=AAAAAA
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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17 ##readme=BBBBBB
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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18 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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19 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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20 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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21 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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23 1 3000000 . C G 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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24 1 3000150 . C G 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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25 1 3000151 . C G 59.2 PASS AN=4;AC=2 GT:DP:GQ 0/1:32:245 0/1:32:245
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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26 1 3106154 . C CCC 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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27 1 3106154 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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28 1 3200000 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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29 1 3200010 . c A,T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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30 1 3200020 . C T,G 59.2 PASS AN=4;AC=2 GT:GL ./.:1,4,6,2,5,3 .:1,3,2