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samtools-index(1)	     Bioinformatics tools	     samtools-index(1)

NAME
       samtools	index -	indexes	SAM/BAM/CRAM files

SYNOPSIS
       samtools	index [-bc] [-m	INT] aln.bam|aln.cram [out.index]

DESCRIPTION
       Index  a	 coordinate-sorted  BGZIP-compressed SAM, BAM or CRAM file for
       fast random access.  (Note that this does not  work  with  uncompressed
       SAM files.)

       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; and for a	compressed SAM
       file aln.sam.gz,	either aln.sam.gz.bai or aln.sam.gz.csi	will  be  cre-
       ated, depending on the index format selected.

OPTIONS
       -b      Create a	BAI index.  This is currently the default when no for-
	       mat options are used.

       -c      Create a	CSI index.  By default,	the minimum interval size  for
	       the index is 2^14, which	is the same as the fixed value used by
	       the BAI format.

       -m INT  Create a	CSI index, with	a minimum interval size	of 2^INT.

AUTHOR
       Written by Heng Li from the Sanger Institute.

SEE ALSO
       samtools(1), samtools-idxstats(1), samtools-view(1)

       Samtools	website: <http://www.htslib.org/>

samtools-1.10			6 December 2019		     samtools-index(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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