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 created, depending on the index format selected.

OPTIONS

       -b      Create a BAI index.  This is currently the default when no format 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/>