NAME

       samtools-index - indexes SAM/BAM/CRAM files

SYNOPSIS

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

DESCRIPTION

       Index  a  coordinate-sorted BGZIP-compressed SAM, BAM or CRAM file for fast random access.
       Note for SAM this only works if the file has been BGZF compressed first.

       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.

       The  BAI  index  format  can  handle  individual chromosomes up to 512 Mbp (2^29 bases) in
       length.  If your input file might contain reads mapped to positions greater than that, you
       will need to use a CSI index.

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.

       -@, --threads INT
               Number of input/output compression threads to use in addition to main thread [0].

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/>