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2026-03-05 15:50:27
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SAMtools SAMtools Home General Information SAM Spec v1.4 SF Project Page SF Download Page GitHub Project Page Mailing Lists Related Software FAQ SAMtools in C General Introduction Manual Pages Variant Calling (mpileup) Text Alignment Viewer API Documentation Example C Program Working on a Stream Open Tasks Var Calling (deprecated) Pileup (deprecated) Variant Call Format Tabix Other Lang-bindings BamTools (C++) Picard (Java) Bio-SamTools (Perl) Pysam (Python) Samtools-Ruby (Ruby) cl-sam (Common Lisp) Samtools-iteratee (Haskell) See http://htslib.org/ for the new 1.x releases of SAMtools, BCFtools, and HTSlib. This website contains information pertaining to the old 0.1.19 samtools release, and so is useful but somewhat out of date. As time permits, this information will be updated for the new samtools/bcftools versions and moved to the new website. Introduction SAM (Sequence Alignment/Map) format is a generic for...
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