Introduction

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM is described in the SAMtools project page.

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (HTSJDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

Picard does not have its own mailing lists. Please use the SAMTools mailing Lists for Picard-related correspondence.

Picard is hosted by SourceForge.net. The project page is here.

The source code for Picard is available on GitHub here. You can check out the latest source code with:

git clone git@github.com:broadinstitute/picard.git

The source code for HTSJDK is available on GitHub here. You can check out the latest source code with:

git clone git@github.com:samtools/htsjdk.git

Getting Help

Picard is supported through the SAMTools mailing Lists. Join samtools-help to get support for Picard programs, and samtools-devel to get support for Picard API.

Before Asking For Help

Before emailing the samtools-help list, please do the following:

When sending email about a problem, please include the following: