Hard filters (by GATK)

 

Filter	Symbol	T.	Definition
QualByDepth	QD	2.0	The variant confidence (from the QUAL field) divided by the unfiltered depth of non-reference samples.
FisherStrand	FS	60.0	Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation being seen on only the forward or only the reverse strand) in the reads.
RMSMappingQuality	MQ	40.0	The Root Mean Square of the mapping quality of the reads across all samples.
HaplotypeScore	HS	13.0	The consistency of the site with two (and only two) segregating haplotypes.
MappingQualityRankSumTest	MQRankSum	12.5	The U-based z-approximation from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele).
ReadPosRankSumTest	ReadPosRankSum	8.0	The U-based z-approximation from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele.

转载于:https://www.cnblogs.com/xingli/p/3582575.html