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/>

samtools-1.13                                      7 July 2021                                 samtools-index(1)