gatk
Link to section 'Description' of 'gatk' Description
Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data
Link to section 'Versions' of 'gatk' Versions
- Anvil: 4.1.8.1
Link to section 'Commands' of 'gatk' Commands
- gatk
Link to section 'Module' of 'gatk' Module
You can load the modules by:
module load gatk
Link to section 'Example job' of '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