picard

Version:

2.27.1, 2.0.1

Category:

bio

Cluster:

Loki

Author / Distributor

https://broadinstitute.github.io/picard/ https://github.com/broadinstitute/picard

Description

Picard is a set of command-line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM, BAM, and VCF. It is written in Java and developed by the Broad Institute, and is commonly used in next-generation sequencing (NGS) workflows.

Documentation

$ java -jar $PICARD/picard.jar -h

or if wrapper is available:

$ picard -h

Common tools:
  MarkDuplicates
  CollectAlignmentSummaryMetrics
  AddOrReplaceReadGroups
  BuildBamIndex
  MergeSamFiles

Version check:
  $ java -jar $PICARD/picard.jar --version

Full docs:
https://broadinstitute.github.io/picard/

Examples/Usage

• Load Picard (version 2.27.1):

$ module load bio/picard/2.27.1

• Mark PCR duplicates in a BAM file:

$ java -jar $PICARD/picard.jar MarkDuplicates \
  I=input.bam O=marked_duplicates.bam M=metrics.txt

• Add or replace read groups:

$ java -jar $PICARD/picard.jar AddOrReplaceReadGroups \
  I=input.bam O=rg_added.bam \
  RGID=1 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=sample1

• Generate alignment summary metrics:

$ java -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics \
  R=reference.fasta I=alignment.bam O=summary.txt

• Unload the module:

$ module unload bio/picard/2.27.1

Installation

Source: https://github.com/broadinstitute/picard/releases/tag/2.0.1