Htsjdk statistics

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Protocols

Htsjdk specifications

Information


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

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Documentation


Additional information


https://github.com/samtools/htsjdk

Htsjdk citations

 (3)
library_books

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

2017
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 (http://samtools.github.io/htsjdk/), 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 […]

call_split

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

2017
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 (http://samtools.github.io/htsjdk/)., 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, […]

library_books

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

2015
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 https://github.com/lindenb/jvarkit/wiki/minicaller. 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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