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samtools index [-bc] [-m INT] aln.bam|aln.cram [out.index] Index a coordinate-sorted BAM or CRAM file for fast random access. (Note that this does not work with SAM files even if they are bgzip compressed — to index such files, use tabix(1) instead.) This index is needed when region arguments are used to limit samtools view and similar commands to particular regions of interest. If an output filename is given, the index file will be written to out.index. Otherwise, for a CRAM file aln.cram, index file aln.cram.crai will be created; for a BAM file aln.bam, either aln.bam.bai or aln.bam.csi will be created, depending on the index format selected.
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  • HL
    Heng Li

    wrote most of the initial source codes of SAMtools and various converters.

  • BH
    Bob Handsaker

    A major contributor to the SAM/BAM specification. He designed and implemented the BGZF format, the underlying indexable compression format for the BAM format. BGZF does not support arithmetic between file offsets.

  • JR
    Jue Ruan

    Designed and implemented the RAZF format, an alternative indexable compression format. RAZF is no longer used by or provided with SAMtools. Source code remains available in older SAMtools 0.1.x releases and from the standalone branch in the repository.

  • CH
    Colin Hercus

    updated to support gapped alignment by novoalign.

  • PD
    Petr Danecek

    contributed the header parsing library sam_header.c and script.