= Interpreting VCF files =

The [http://vcftools.sourceforge.net/specs.html 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 ||