vcf(5) - f39

1vcf(5)                      Bioinformatics formats                      vcf(5)
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NAME

6       vcf - Variant Call Format
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DESCRIPTION

9       The  Variant Call Format (VCF) is a TAB-delimited format with each data
10       line consisting of the following fields:
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12        1    CHROM    CHROMosome name
13        2    POS      the left-most POSition of the variant
14        3    ID       unique variant IDentifier
15        4    REF      the REFerence allele
16        5    ALT      the ALTernate allele(s) (comma-separated)
17        6    QUAL     variant/reference QUALity
18        7    FILTER   FILTERs applied
19        8    INFO     INFOrmation related to the variant (semicolon-separated)
20        9    FORMAT   FORMAT of the genotype fields (optional; colon-separated)
21       10+   SAMPLE   SAMPLE genotypes and per-sample information (optional)
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23       The following table gives the INFO tags used by samtools and bcftools.
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25       AF1    Max-likelihood estimate of the site allele frequency (AF) of the
26              first ALT allele (double)
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28       DP     Raw read depth (without quality filtering) (int)
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30       DP4    #  high-quality  reference forward bases, ref reverse, alternate
31              for and alt rev bases (int[4])
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33       FQ     Consensus quality. Positive: sample genotypes  different;  nega‐
34              tive: otherwise (int)
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36       MQ     Root-Mean-Square mapping quality of covering reads (int)
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38       PC2    Phred   probability   of  AF  in  group1  samples  being  larger
39              (,smaller) than in group2 (int[2])
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41       PCHI2  Posterior weighted chi^2 P-value between group1 and group2  sam‐
42              ples (double)
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44       PV4    P-value for strand bias, baseQ bias, mapQ bias and tail distance
45              bias (double[4])
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47       QCHI2  Phred-scaled PCHI2 (int)
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49       RP     # permutations yielding a smaller PCHI2 (int)
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51       CLR    Phred log ratio of genotype likelihoods  with  and  without  the
52              trio/pair constraint (int)
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54       UGT    Most probable genotype configuration without the trio constraint
55              (string)
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57       CGT    Most probable configuration with the trio constraint (string)
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59       VDB    Tests variant positions within  reads.  Intended  for  filtering
60              RNA-seq artifacts around splice sites (float)
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62       RPB    Mann-Whitney rank-sum test for tail distance bias (float)
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64       HWE    Hardy-Weinberg equilibrium test (Wigginton et al) (float)
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NAME

DESCRIPTION

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