vcf: Variant call format

DESCRIPTION

The Variant Call Format (VCF) is a TAB-delimited format with each data line consisting of the following fields:

1
CHROM
CHROMosome name
2
POS
the left-most POSition of the variant
3
ID
unique variant IDentifier
4
REF
the REFerence allele
5
ALT
the ALTernate allele(s) (comma-separated)
6
QUAL
variant/reference QUALity
7
FILTER
FILTERs applied
8
INFO
INFOrmation related to the variant (semicolon-separated)
9
FORMAT
FORMAT of the genotype fields (optional; colon-separated)
10+
SAMPLE
SAMPLE genotypes and per-sample information (optional)

The following table gives the INFO tags used by samtools and bcftools.

AF1: Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele (double)
DP: Raw read depth (without quality filtering) (int)
DP4: # high-quality reference forward bases, ref reverse, alternate for and alt rev bases (int[4])
FQ: Consensus quality. Positive: sample genotypes different; negative: otherwise (int)
MQ: Root-Mean-Square mapping quality of covering reads (int)
PC2: Phred probability of AF in group1 samples being larger (,smaller) than in group2 (int[2])
PCHI2: Posterior weighted chi^2 P-value between group1 and group2 samples (double)
PV4: P-value for strand bias, baseQ bias, mapQ bias and tail distance bias (double[4])
QCHI2: Phred-scaled PCHI2 (int)
RP: # permutations yielding a smaller PCHI2 (int)
CLR: Phred log ratio of genotype likelihoods with and without the trio/pair constraint (int)
UGT: Most probable genotype configuration without the trio constraint (string)
CGT: Most probable configuration with the trio constraint (string)
VDB: Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites (float)
RPB: Mann-Whitney rank-sum test for tail distance bias (float)
HWE: Hardy-Weinberg equilibrium test (Wigginton et al) (float)