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/>

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