Picard Tools

Introduction

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. Detailed usage can be found here: https://broadinstitute.github.io/picard/

Versions

2.25.1
2.26.10

Commands

picard

Module

You can load the modules by:

module load biocontainers
module load picard/2.26.10

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run picard our our clusters:

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

module --force purge
ml biocontainers picard/2.26.10

picard MarkDuplicates -Xmx64g I=19P0126636WES_sorted.bam O=19P0126636WES_sorted_md.bam M=19P0126636WES.sorted.markdup.txt REMOVE_DUPLICATES=true
picard BuildBamIndex -Xmx64g I=19P0126636WES_sorted_md.bam
picard CreateSequenceDictionary -R hg38.fa -O hg38.dict