snvListVCF: Generate a VCF with the information from the SNPs that pass a...

In belleau/aicsPaper: Accurate Inference of Genetic Ancestry from Cancer Sequencing

Generate a VCF with the information from the SNPs that pass a cut-off threshold

Description

This function extract the SNPs that pass a frequency cut-off in at least one super population from a GDS SNP information file and save the retained SNP information into a VCF file.

Usage

snvListVCF(gds, fileOUT, offset = 0L, freqCutoff = NULL)

Arguments

gds	an object of class SNPRelate::SNPGDSFileClass, a SNP GDS file.
fileOUT	a character string representing the path and file name of the VCF file that will be created wit the retained SNP information.
offset	a single integer that is added to the SNP position to switch from 0-based to 1-based coordinate when needed (or reverse). Default: 0L.
freqCutoff	a single positive numeric specifying the cut-off to keep a SNP. If NULL, all SNPs are retained. Default: NULL.

Value

The integer 0 when successful.

Author(s)

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples

## Path to the demo pedigree file is located in this package
data.dir <- system.file("extdata", package="RAIDS")

## TODO

belleau/aicsPaper documentation built on Aug. 4, 2022, 1:12 a.m.