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1 ##fileformat=VCFv4.1
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2 ##FILTER=<ID=PASS,Description="All filters passed">
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3 ##reference=file:///seq/references/1000Genomes-NCBI37.fasta
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4 ##contig=<ID=11,length=135006516>
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5 ##contig=<ID=20,length=63025520>
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6 ##contig=<ID=X,length=155270560>
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7 ##contig=<ID=Y,length=59373566>
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8 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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9 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
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10 ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of reads containing spanning deletions">
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11 ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
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12 ##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest contiguous homopolymer run of variant allele in either direction">
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13 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Hardy-Weinberg equilibrium test (PMID:15789306)">
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14 ##INFO=<ID=ICF,Number=1,Type=Float,Description="Inbreeding coefficient F">
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15 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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16 ##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
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17 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
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18 ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total mapping quality zero reads">
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19 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
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20 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth">
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21 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
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22 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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23 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
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24 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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25 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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26 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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27 ##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
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28 ##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
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29 ##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
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30 ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
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31 ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
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32 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003
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33 X 2928329 rs62584840 C T 999 PASS DP4=302,9137,32,1329;DP=11020;Dels=0;FS=13.38;HWE=0.284332;ICF=0.0253;MQ0=0;MQ=49;PV4=0.094,0,0,1;QD=18.61;AN=2;AC=1 GT:PL:DP:GQ 0/1:73,0,19:4:30
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34 X 2933066 rs61746890 G C 999 PASS DP4=69865,100561,461,783;DP=173729;Dels=0;FS=10.833;MQ0=0;MQ=50;PV4=0.005,3.6e-14,0,1;QD=15.33;AN=2;AC=1 GT:PL:DP:GQ 0/1:255,255,255:62:99
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