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description=Samtools organisation for next-generation sequencing developers: htslib C API, htsjdk Java API, file format specifications, and samtools/bcftools source code.;

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api, file, format, specifications, and, high, throughput, sequencing, tools, java,

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samtools repositories samtools organisation and repositories samtools at github is an umbrella organisation encompassing several groups working on formats and tools for next generation sequencing file format specifications the hts specs repository contains the specifications of several sequence data formats sam bam and cram variant calling data formats vcf and bcf feature data formats bed and related formats such as indexing encryption and transfer protocols changes to these formats are discussed as issues and pull requests there c api and high throughput sequencing tools the htslib repository contains a c api and library for manipulating these formats the bcftools and samtools repositories contain c programs for manipulating these formats on the command line and for performing variant calling java api the htsjdk repository contains a java api for manipulating these formats htsjdk is used by the picard tools hosted elsewhere there are also several other historical repositories within the samtools organisation containing tools and source code that have since been integrated into htslib or that have been deprecated and remain available mainly for their historical interest samtools samtools organisation for next generation sequencing developers htslib c api htsjdk java api file format specifications and samtools bcftools source code