GATK4-4.1.0.0 ¶

Table of Contents

GATK4-4.1.0.0

Basic Information ¶

Deploy date: 2 January 2019
Official Website: https://software.broadinstitute.org/gatk/documentation/quickstart
License: GATK4 License
Installed on: Apolo II

Installation ¶

This entry covers the entire process performed for the installation GATK4 on a cluster.

Usage ¶

This section describes the method to submit jobs with the resource manager SLURM.

Load the necessary environment.
```
module load gatk4/4.1.0.0
```

Run GATK4 with SLURM.

An example:

For this example, we use the GATK tutorial Run the Pathseq pipeline

gatk.sh¶

#!/bin/sh                                                                                                                                                                                                                                     

#SBATCH --partition=longjobs                                                                                                                                                                                                                  
#SBATCH --nodes=1                                                                                                                                                                                                                             
#SBATCH --ntasks-per-node=1                                                                                                                                                                                                                   
#SBATCH --time=05:00                                                                                                                                                                                                                          
#SBATCH --job-name=gatk_example                                                                                                                                                                                                               
#SBATCH -o gatk4_%j.out                                                                                                                                                                                                                   
#SBATCH -e gatk4_%j.err                                                                                                                                                                                                                   
#SBATCH --mail-type=END,FAIL                                                                                                                                                                                                                  
#SBATCH --mail-user=youremail@email.com

# Don't share environment variables                                                                                                                                                                                                           

module load gatk4/4.1.0.0

gatk PathSeqPipelineSpark \
    --input test_sample.bam \
    --filter-bwa-image hg19mini.fasta.img \
    --kmer-file hg19mini.hss \
    --min-clipped-read-length 70 \
    --microbe-fasta e_coli_k12.fasta \
    --microbe-bwa-image e_coli_k12.fasta.img \
    --taxonomy-file e_coli_k12.db \
    --output output.pathseq.bam \
    --scores-output output.pathseq.txt

Note

If you want to run some tests, go to the GATK4 page with tutorials.

Authors ¶

Manuela Carrasco Pinzón <mcarras1@eafit.edu.co>

GATK4-4.1.0.0¶

Basic Information¶

Installation¶

Usage¶

Authors¶