VCFData-class: Declare class Reads in VCF using readVCFAsVRanges

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

Description

Declare class Reads in VCF using readVCFAsVRanges

Arguments

mydir	Directory of vcf file
myfile	Filename of vcf file
vr.homref	All SNPs from VCF with INDELs, MULTIs (seperately removed for variant and non variant), weird chromosomes removed
genoString	A character vector of all genotype fields present (looks for AD, GQ, GT, DP)
infoString	A character vector looking for "END" tag indicating file is a gVCF
genome	Declare if the genome is GRCh37 or GRCh38
n.dup	Counts the number of MULTIs removed
chunked	Whether data was read in using ReadVCFDataChunk which means hom refs not in the admixture file were dropped

Value

Object of class VCFData

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