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Table 5 Parameters and their thresholds selected by regression trees

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

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
  1. (*): no reliable filters were selected by classification trees