Htsjdk statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Htsjdk

Tool usage distribution map

This map represents all the scientific publications referring to Htsjdk per scientific context
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Associated diseases

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Htsjdk specifications


Unique identifier OMICS_19951
Name Htsjdk
Software type Framework/Library
Interface Application programming interface
Restrictions to use None
Input format SAM, VCF
Output format SAM, VCF
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes




Additional information

Htsjdk citation


Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single stranded Virus Next generation Sequencing

Mol Ther Nucleic Acids
PMCID: 4881760
PMID: 26506038
DOI: 10.1038/mtna.2015.32

[…] (but more robust) callers. The source code for this java program is available on GitHub at Essentially, this program uses the java library for BAM (htsjdk) to load a set of BAM files and scans all of the bases in the reference genome from 5′ to 3′; for each position, it detects the proportion of bases in each sample and prints a summary in VCF fo […]

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