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.

Please see the HTSJDK Documentation for more information.

Licensing Information

Not all sub-packages of htsjdk are subject to the same license, so a license notice is included in each source file or sub-package as appropriate. Please check the relevant license notice whenever you start working with a part of htsjdk that you have not previously worked with to avoid any surprises.

Java Minimum Version Support Policy

NOTE: Effective November 24th 2015, HTSJDK has ended support of Java 7 and previous versions. Java 8 is now required.

We will support all Java SE versions supported by Oracle until at least six months after Oracle's Public Updates period has ended (see this link).

Java SE Major Release	End of Java SE Oracle Public Updates	Proposed End of Support in HTSJDK	Actual End of Support in HTSJDK
6	Feb 2013	Aug 2013	Oct 2015
7	Apr 2015	Oct 2015	Oct 2015
8*	Mar 2017	Sep 2017	Sep 2017

• to be finalized