Download

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported. A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.

Picard is implemented using the HTSJDK Java library HTSJDK to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM and VCF.

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.

Building Picard with a Custom Version of HTSJDK
During development in Picard, it is sometimes necessary to build locally against an unreleased version or branch of HTSJDK.

To build against an unreleased version of HTSJDK's master branch:

Go to the Broad artifactory, where continuous snapshots of HTSJDK's master branch are published, and select the version you want to use. For example, 2.5.1-9-g5740ca1-SNAPSHOT. You can search by tag or short git commit hash.
In your Picard clone, run ./gradlew shadowJar -Dhtsjdk.version=VERSION, where VERSION is the version of the HTSJDK master branch snapshot you want to use.
To build against a version of HTSJDK that has not yet been merged into HTSJDK's master branch:

Clone HTSJDK, and in your clone check out the tag or branch you want to build Picard with.
Run ./gradlew install printVersion in your htsjdk clone to install that version to your local maven repository. Take note of the version number that gets printed at the end.
Switch back to your Picard clone, and run ./gradlew shadowJar -Dhtsjdk.version=VERSION, where VERSION is the version of HTSJDK you installed to your local maven repository.