Table 2 SNP statistics reported by GATK and thresholds used for filtering
From: Positional bias in variant calls against draft reference assemblies
Abbreviation | Rel | Threshold | Full name |
|---|---|---|---|
QD | < | 2.0 | Quality by Depth |
MQ | < | 40.0 | Root mean square of Mapping Quality |
MQRankSum | < | −12.5 | Mapping Quality Rank Sum test |
FS | > | 60.0 | Fisher’s exact test for Strand bias |
SOR | > | 4.0 | Strand bias Odds Ratio |
ReadPosRankSum | < | −8.0 | Read Position Rank Sum test |
DP | > | 200.0 | Depth of Coverage |
GQ | < | 20.0 | Genotype Quality |