genotypeeval (version 1.2.2)

VCFData-class: Declare class Reads in VCF using readVCFAsVRanges

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