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/
- 2.25.1
- 2.26.10
picard
You can load the modules by:
module load biocontainers module load picard/2.26.10
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