/GATK-gVCF-header

Description of a typical gVCF

Header of a GATK-based gVCF file

Description of a typical gVCF (fileformat=VCFv4.2).


ALT

Represents any possible alternative allele at this location.
NON_REF.


FILTER section

LowQual.
Low quality


INFO section

AC

Allele count in genotypes, for each ALT allele, in the same order as listed.
Number=A
Type=Integer


AF

Allele Frequency, for each ALT allele, in the same order as listed.
Number=A
Type=Float


AN

Total number of alleles in called genotypes.
Number=1
Type=Integer


BaseQRankSum

Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities.
Number=1
Type=Float


ClippingRankSum

Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases.
Number=1
Type=Float


DP

Approximate read depth; some reads may have been filtered.
Number=1
Type=Integer


DS

Were any of the samples downsampled? Number=0
Type=Flag


END

Stop position of the interval.
Number=1
Type=Integer


ExcessHet

Phred-scaled p-value for exact test of excess heterozygosity.
Number=1
Type=Float


FS

Phred-scaled p-value using Fisher's exact test to detect strand bias.
Number=1
Type=Float


HaplotypeScore

Consistency of the site with at most two segregating haplotypes.
Number=1
Type=Float


InbreedingCoeff

Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation.
Number=1
Type=Float


MLEAC

Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed.
Number=A
Type=Integer


LEAF

Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed.
Number=A
Type=Float


MQ

RMS Mapping Quality.
Number=1
Type=Float


MQRankSum

Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities.
Number=1
Type=Float


QD

Variant Confidence/Quality by Depth.
Number=1
Type=Float


RAW_MQ

Raw data for RMS Mapping Quality.
Number=1
Type=Float


ReadPosRankSum

Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias.
Number=1
Type=Float


SOR

Symmetric Odds Ratio of 2x2 contingency table to detect strand bias.
Number=1
Type=Float


FORMAT section

AD

Allelic depths for the ref and alt alleles in the order listed.
Number=R
Type=Integer


DP

Approximate read depth (reads with MQ=255 or with bad mates are filtered).
Number=1
Type=Integer


GQ

Genotype Quality.
It corresponds to the difference of the two most probable genotypes (since the most probable is assigned a '0', the lowest, likelihood).
Number=1
Type=Integer


GT

Genotype.
Number=1
Type=String


MIN_DP

Minimum DP observed within the GVCF block.
Number=1
Type=Integer


PGT

Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another.
Number=1
Type=String


PID

Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group.
Number=1
Type=String


PL

Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification.
Number=G
Type=Integer


RGQ

Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong).
Number=1
Type=Integer


SB

Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.
Number=4
Type=Integer