gatk

Description

Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data

Versions

• Anvil: 4.1.8.1

Module

You can load the modules by:

module load gatk

Example job

To run gatk our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH -p PartitionName
#SBATCH --job-name=gatk
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module load gatk

gatk  --java-options "-Xmx12G -XX:ParallelGCThreads=24" HaplotypeCaller -R hg38.fa -I 19P0126636WES.sorted.bam  -O 19P0126636WES.HC.vcf --sample-name 19P0126636