PureCN (version 1.0.3)

filterVcfBasic: Basic VCF filter function

Description

Function to remove artifacts and low confidence/quality variant calls.

Usage

filterVcfBasic(vcf, tumor.id.in.vcf = NULL, use.somatic.status = TRUE, 
    snp.blacklist = NULL, af.range = c(0.03, 0.97), 
    contamination.cutoff = c(0.05, 0.075), coverage.cutoff = 20, 
    min.supporting.reads = 3, verbose = TRUE)

Arguments

vcf

CollapsedVCF object, read in with the readVcf function from the VariantAnnotation package.

tumor.id.in.vcf

The tumor id in the CollapsedVCF (optional).

use.somatic.status

If somatic status and germline data is available, then use this information to remove non-heterozygous germline SNPs or germline SNPS with biased allelic fractions.

snp.blacklist

CSV file with SNP ids with expected allelic fraction significantly different from 0.5 in diploid genomes. Can be an array of lists. The function createSNPBlacklist can provide appropriate black lists.

af.range

Exclude SNPs with allelic fraction smaller or greater than the two values, respectively.

contamination.cutoff

Count SNPs in dbSNP with allelic fraction smaller than the first value, if found on most chromosomes, remove all with AF smaller than the second value.

coverage.cutoff

Minimum coverage in tumor. Variants with lower coverage are ignored.

min.supporting.reads

Minimum number of reads supporting the alt allele.

verbose

Value

• A list with elements
• vcf
  The filtered CollapsedVCF object.
• flag
  A flag (TRUE/FALSE) if problems were identified.
• flag_comment
  A comment describing the flagging.

Examples

# This function is typically only called by runAbsolute via the 
# fun.filterVcf and args.filterVcf comments.
library(VariantAnnotation)    
vcf.file <- system.file("extdata", "example_vcf.vcf", package="PureCN")
vcf <- readVcf(vcf.file, "hg19")
vcf.filtered <- filterVcfBasic(vcf)

Run the code above in your browser using DataCamp Workspace