writeToVCF: exports variants to VCF

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

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')

## End(Not run)

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.