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picard

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/

Link to section 'Versions' of 'picard' Versions

  • 2.25.1
  • 2.26.10

Link to section 'Commands' of 'picard' Commands

picard

Link to section 'Module' of 'picard' Module

You can load the modules by:

module load biocontainers
module load picard/2.26.10 

Link to section 'Example job' of 'picard' Example job

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
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