groupChr1KGSNV: Merge the genotyping files per chromosome into one file

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

Merge the genotyping files per chromosome into one file

Description

This function merge all the genotyping files associated to one specific sample into one file. That merged VCF file will be saved in a specified directory and will have the name of the sample. It will also be compressed (bzip). The function will merge the files for all samples present in the input directory.

Usage

groupChr1KGSNV(PATHGENOCHR, PATHOUT)

Arguments

PATHGENOCHR	a character string representing the path where the genotyping files for each sample and chromosome are located. The path must contains sub-directories (one per chromosome) and the genotyping files must be present in those sub-directories. The path must exists.
PATHOUT	a character string representing the path where the merged genotyping files for each sample will be created. The path must exists.

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.