VCFQAParam-class: Declare class VCFQAParam which will store thresholds to apply...

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

Description

Declare class VCFQAParam 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

homref.limits	lower limit, upper limit, number of homozygous reference
het.limits	lower limit, upper limit, number of heterozygous calls
homvar.limits	lower limit, upper limit, number of homozygous alternative
count.limits	lower limit, upper limit, total number of counts
percenthets.limits	lower limit, upper limit, Number of Heterozgyous / (Total Number of Counts) or percent het
titv.noncoding.limits	lower limit, upper limit, Transition transversion ratio in noncoding regions
titv.coding.limits	lower limit, upper limit, Transition transversion ratio in coding regions
readdepth.target	The sequencing depth target (eg 30x)
readdepth.limits	lower limit, upper limit, Mean read depth
readdepth.percent.limits	lower limit, upper limit, Percent read depth in target (50 percent to 200 percent of target read depth)
gq.limit	lower limit, Mean genotype quality (does not make sense to have an upper limit)
masked.limits	lower limit, upper limit, (Number of heterozygous in masked regions)/(Total number of heterozygotes)
non.masked.limits	lower limit, upper limit, (Number of heterozygous in non-self chained regions)/(Total number of heterozygotes)
het.gap.limits	lower limit, upper limit, Largest gap within chromosome between two heterozygous calls
gq.filter	filter for the VCF file on genotype quality (eg only GQ > 90)
dp.filter	filter for the VCF file on read depth (eg only DP > 0)

Value

VCFQAParam object

jentom/genotypeeval documentation built on May 13, 2019, 12:54 p.m.