Htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.

• Getting help
• HTSJDK Github Project Page
• SAMTools Home Page
• SAM Format Specification
• SAMTools mailing Lists
• Explain SAM Flags

• Example
• Building
• Javadoc