PureCN (version 1.0.3)

createSNPBlacklist: Create SNP black list

Description

Function to create a black list of germline SNPs with expected allelic fraction (AF) smaller than 0.5 in diploid genomes.

Usage

createSNPBlacklist(vcf.files, n = min(10, length(vcf.files)), 
    low.af = 0.025, high.af = 0.1, genome = "hg19")

Arguments

vcf.files

List of VCF files. When a VCF file contains multiple samples, it will ignore all samples except the first.

n

Required number of VCF files showing low allelic fraction to blacklist a SNP id.

low.af

Defines a low AF p-value.

high.af

Defines a high AF p-value. For every sample with high AF p-value, there must be one more sample with low AF to reach the cutoff.

genome

Version of the reference genome, required for the readVcf() function.

Value

• A list with elements snp.black.list and segmented. "snp.black.list" is just a list of SNP ids. "segmented" blacklists whole regions.

Examples

# Assume VCF files of normals (for example obtained by a MuTect artifact
# detection run) are in directory poolofnormals:
mutect.normal.files <- dir("poolofnormals", pattern="vcf$", full.names=TRUE) 

# These files do not exist in our example, so we do not run the function here.
#snp.blacklist <- createSNPBlacklist(mutect.normal.files)