Interpreting VCF files

The ​VCF (Variant Call Format) specification describes most of what you need to know.

Tags in the FILTER, INFO, and FORMAT fields are described in the VCF header.

As a tabular reference, common tags are as follows:

FILTER field (typically generated by vcf-annotate):

Tag	Description	Default threshold
BaseQualBias	Min P-value for baseQ bias	0
EndDistBias	Min P-value for end distance bias	0.0001
GapWin	Window size for filtering adjacent gaps	3
MapQualBias	Min P-value for mapQ bias	0
MaxDP	Maximum read depth	10000000
MinAB	Minimum number of alternate bases	2
MinDP	Minimum read depth	2
MinMQ	Minimum RMS mapping quality for SNPs	10
Qual	Minimum value of the QUAL field	10
RefN	Reference base is N	[]
SnpGap	SNP within INT bp around a gap to be filtered	10
StrandBias	Min P-value for strand bias	0.0001
VDB	Minimum Variant Distance Bias	0