update_vcf: Remove CNV regions within VCF files

In vanquish: Variant Quality Investigation Helper

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

vanquish documentation built on May 2, 2019, 9:42 a.m.