superFreq (version 1.2.3)

writeToVCF: exports variants to VCF

Description

exports variants to VCF

Usage

writeToVCF(q, vcfFile, genome = "hg19", snvOnly = F, addSomaticP = F)

Arguments

q

A variant data frame from superFreq.

vcfFile

The path to the output file.

genome

The genome, such as 'hg19', 'hg38' or 'mm10'. Defaults to 'hg19'.

addSomaticP

boolean. Set to TRUE to include a column with the somaticP score from superFreq. Defaults to FALSE.

SNVonly

boolean. Set to TRUE to only output SNVs, not indels. Defaults to FALSE.

Details

This function outputs superFreq variants to a VCF for access from other software.

Examples

# NOT RUN {
data = loadData(Rdirectory)
q = data$allVariants$variants$variants$mySample
writeToVCF(q, 'mySample.superFreq.vcf')
# }