numberCalls: Total Calls. This is the total number of calls in the file...

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

Description

Total Calls. This is the total number of calls in the file (including MULTIs so hom ref, hom var and hom alt might not add up). These methods are private. Users are not expected to provide the number of hom ref and number of duplicate calls - these functions are generally called through the function VCFEvaluate

Usage

numberCalls(x, n.hom, n.dup, ll, ul)

Arguments

x	myvcf of interest
n.hom	Number of homozygous reference. Pass so don't need to recalculate
n.dup	number of multi calls to add onto the total calls
ll	lower limit to pass for hom ref
ul	upper limit to pass for hom ref

Value

list with name, logical (passed or not), numeric (total number of calls)

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