update_vcf {vanquish}

Remove CNV regions within VCF files

Description

Remove CNV regions within VCF files

Usage

update_vcf(rmCNV = FALSE, vcf, cnvobj = NULL, threshold = 0.1,
  skew = 0.5, lower = 0.45, upper = 0.55)

Arguments

rmCNV

Remove CNV regions, default is FALSE

vcf

Input VCF files

cnvobj

cnv object, default is NULL

threshold

Threshold for allele frequency, default is 0.1

skew

Skewness for allele frequency, default is 0.5

lower

Lower bound for allele frequency region, default is 0.45

upper

Upper bound for allele frequency region, default is 0.55

Value

VCF file without CNV region