GoldDataParam-class: Declare class GoldDataParam which will store thresholds to...

In genotypeeval: QA/QC of a gVCF or VCF file

Description

Declare class GoldDataParam which will store thresholds to apply to VCFEvaluate object. This is intended for use in batch mode when a large number of vcf files needs to be screened and individual vcf files that fail flagged. All limits follow the format lower limit than upper limit

Arguments

titv.confirmed.limits	lower limit coding, upper limit coding, lower limit noncoding, upper limit noncoding, Transition transversion ratios for confirmed snps
titv.unconfirmed.limits	lower limit coding, upper limit coding, lower limit noncoding, upper limit noncoding, Transition transversion ratios for unconfirmed snps
percent.confirmed.limits	lower limit, upper limit, percent confirmed in Gold comparator
percent.het.rare.limits	lower limit, upper limit, (Percent Het in Rare, MAF < 0.01 in Gold) / Total number of Heterozygotes

Value

Object of type GoldDataParam

genotypeeval documentation built on Nov. 8, 2020, 5:03 p.m.