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.
The source code for Picard is available on GitHub here. You can check out the latest source code with:
git clone email@example.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 firstname.lastname@example.org:samtools/htsjdk.git
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:
- Try the latest version of Picard
- See if your problem is discussed in the FAQ
- Run Picard ValidateSamFile MODE=SUMMARY. Attempt to resolve or at least understand any problems reported.
When sending email about a problem, please include the following:
- Command line(s) you used.
- Program console output and metrics files. Repetitive console output may be abbreviated.
- Entire stack trace if one was produced.
- Version of JVM are you using (obtained by running 'java -version').