GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data

Table 5 Parameters and their thresholds selected by regression trees

Sequencing depth	Variant type	Genotype by GATK	Filter rule
20x	SNV	homozygous	ADT > =0.98
20x	SNV	heterozygous	ADT < 0.55
20x	INDEL	homozygous	N/A (*)
20x	INDEL	heterozygous	ADT < 0.26 & GQ > =98.5 & DP > =23.5 & MQ > =59.5 ADT < 0.26 & DP > 23.5 & ReadPosRankSum < -1.55
100x	SNV	homozygous	ADT > =0.96
100x	SNV	heterozygous	GQ > =68.5
100x	INDEL	homozygous	ADTL > =5.08
100x	INDEL	heterozygous	ADT < 0.15 & MQ > =59.91 & GQ > =98.5

ISSN: 1471-2105