Mutect2: Detect variants with Mutect2

In honzee/SNPsom: Containerized Somatic Variant Analysis

Detect variants with Mutect2

Description

Run Mutect2 with the option to run multiple samples in parallel. Chekcs for GATK sequence dictionary and samtools index, if the files do not exist, they will be automatically created.

Usage

Mutect2(metadata, input_dir, output_dir, reference, parallel)

Arguments

metadata	data frame;
input_dir	character; path to the input directory
output_dir	character; path to output directory
reference	character; path to the fasta genome reference file. Bwa-mem2 created index must be in the same directory.
t	numeric; number of threads to use; default-2
parallel;	how many samples should be ran in parallel, each one will need around 15 GB of RAM

honzee/SNPsom documentation built on July 27, 2022, 12:45 a.m.