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)
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SAMtools
Sites with less than 20 quality (QUAL)
Genotype calls with less than 5 depth (DP)
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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)
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VarScan
Sites with less than 0.10% minor allele frequency (MAF)
Genotype calls with less than 10 depth (DP)
Heterozygote genotype calls
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Common Filters
Sites not called in both parent and offspring
Sites with greater than 50% missingness
Multiallelic sites
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