FreeBayes Sites with less than 30 quality (QUAL) Genotype calls with less than 10 depth (DP) Genotype calls with less than 20 genotype quality (GQ)
HaplotypeCaller Sites with greater than 60 Fisher strand (FS) Sites with less than 40 mapping quality (MQ) Sites with less than -12.5 mapping quality rank sum test (MQRankSum) Sites with less than 30 quality (QUAL) Sites with less than 2.0 quality by depth (QD) Sites with less than -8.0 read position rank sum test (ReadPosRankSum) Sites with greater than 3.0 strand odds ratio (SOR) Genotype calls with less than 20 genotype quality (GQ)
SAMtools Sites with less than 20 quality (QUAL) Genotype calls with less than 5 depth (DP)
UnifiedGenotyper Sites with greater than 60 Fisher strand (FS) Sites with less than 40 mapping quality (MQ) Sites with less than -12.5 mapping quality rank sum test (MQRankSum) Sites with less than 30 quality (QUAL) Sites with less than 2.0 quality by depth (QD) Sites with less than -8.0 read position rank sum test (ReadPosRankSum) Sites with greater than 3.0 strand odds ratio (SOR)
VarScan Sites with less than 0.10% minor allele frequency (MAF) Genotype calls with less than 10 depth (DP) Heterozygote genotype calls
Common Filters Sites not called in both parent and offspring Sites with greater than 50% missingness Multiallelic sites