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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 citations


Hepatocytic expression of human sodium taurocholate cotransporting polypeptide enables hepatitis B virus infection of macaques

PMCID: 5732258
PMID: 29247188
DOI: 10.1038/s41467-017-01953-y

[…] around indels was performed using gatk. nucleotide difference between reads and the reference sequences were scored using custom software that utilized hts-jdk (, and amino acid translations were performed that accounted for read-specific flanking sequence., a single lobe of non-human primate liver was perfused with 250 ml of hanks balanced salt […]


Allogeneic stem cell transplantation in fully MHC matched Mauritian cynomolgus macaques recapitulates diverse human clinical outcomes

PMCID: 5681693
PMID: 29127275
DOI: 10.1038/s41467-017-01631-z
call_split See protocol

[…] published mhc sequences using the aligner mosaik, version 2.2–. perfect matches between reads and reference alleles were scored using custom software that utilized hts-jdk (, the initial flu-bu-tbi reduced intensity conditioning regimen consisted of fludarabine (flu, 30 mg/m2 iv on day −4 through day −2, 90 mg/m2 total, manufactured by ben venue laboratories, […]


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

PMCID: 4881760
PMID: 26506038
DOI: 10.1038/mtna.2015.32

[…] 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 […]

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