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annotate test-data/freebayes_out.vcf @ 0:33a0e6aca936 draft default tip

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:27:37 -0500
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1 ##fileformat=VCFv4.0
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2 ##fileDate=20110225
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3 ##source=freeBayes version 0.4.2
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4 ##reference=localref.fa
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5 ##phasing=none
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6 ##commandline="freebayes --fasta-reference localref.fa localbam.bam --vcf /galaxy/home/dannon/galaxy-central/database/files/000/dataset_11.dat"
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7 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
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8 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
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9 ##INFO=<ID=AC,Number=1,Type=Integer,Description="Total number of alternate alleles in called genotypes">
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10 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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11 ##INFO=<ID=AF,Number=1,Type=Float,Description="Estimated allele frequency in the range (0,1]">
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12 ##INFO=<ID=SR,Number=1,Type=Integer,Description="Number of reference observations by strand, delimited by |: [forward]|[reverse]">
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13 ##INFO=<ID=SA,Number=1,Type=Integer,Description="Number of alternate observations by strand, delimited by |: [forward]|[reverse]">
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14 ##INFO=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
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15 ##INFO=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
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16 ##INFO=<ID=SB,Number=1,Type=Float,Description="Strand bias for the alternate allele: a number between 0 and 1 representing the ratio of forward strand sequence reads showing the alternate allele to all reads, considering only reads from individuals called as heterozygous">
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17 ##INFO=<ID=AB,Number=1,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
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18 ##INFO=<ID=ABR,Number=1,Type=Integer,Description="Reference allele balance count: the number of sequence reads from apparent heterozygotes supporting the reference allele">
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19 ##INFO=<ID=ABA,Number=1,Type=Integer,Description="Alternate allele balance count: the number of sequence reads from apparent heterozygotes supporting the alternate allele">
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20 ##INFO=<ID=RUN,Number=1,Type=Integer,Description="Homopolymer run length: the number of consecutive nucleotides in the reference genome matching the alternate allele prior to the current position">
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21 ##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous).">
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22 ##INFO=<ID=SNP,Number=0,Type=Flag,Description="SNP allele">
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23 ##INFO=<ID=TS,Number=0,Type=Flag,Description="transition SNP">
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24 ##INFO=<ID=TV,Number=0,Type=Flag,Description="transversion SNP">
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25 ##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)">
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26 ##INFO=<ID=MNP,Number=0,Type=Integer,Description="Length of MNP allele, if present">
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27 ##INFO=<ID=INS,Number=1,Type=Integer,Description="Length of insertion allele, if present">
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28 ##INFO=<ID=DEL,Number=1,Type=Integer,Description="Length of deletion allele, if present">
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29 ##INFO=<ID=REPEAT,Number=1,Type=String,Description="Description of the local repeat structures flanking the current position">
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30 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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31 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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32 ##FORMAT=<ID=GL,Number=1,Type=Float,Description="Genotype Likelihood">
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33 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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34 ##FORMAT=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
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35 ##FORMAT=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
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36 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of reference observations by strand, delimited by |: [forward]|[reverse]">
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37 ##FORMAT=<ID=SA,Number=1,Type=Integer,Description="Number of alternate observations by strand, delimited by |: [forward]|[reverse]">
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38 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
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39 178508 900 . A C 94 . NS=1;DP=8;AC=1;AN=2;AF=0.5;RA=3;AA=4;SR=3|0;SA=4|0;SB=1;AB=0.42857;ABR=3;ABA=4;RUN=1;BVAR;SNP;TV GT:GQ:GL:DP:RA:AA:SR:SA 1/0:88.541:-1.2967:7:3:4:3|0:4|0
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40 178508 1800 . A C 93.6 . NS=1;DP=10;AC=1;AN=2;AF=0.5;RA=5;AA=4;SR=5|0;SA=4|0;SB=1;AB=0.55556;ABR=5;ABA=4;RUN=1;BVAR;SNP;TV GT:GQ:GL:DP:RA:AA:SR:SA 1/0:93.56:-1.402:9:5:4:5|0:4|0