NAME

       samtools-index - indexes SAM/BAM/CRAM files

SYNOPSIS

       samtools index -M [-bc] [-m INT] FILE FILE [FILE...]

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

DESCRIPTION

       Index  coordinate-sorted  BGZIP-compressed  SAM, BAM or CRAM files for fast random access.
       Note for SAM this only works if the file has  been  BGZF  compressed  first.   (The  first
       synopsis with multiple input FILEs is only available with Samtools 1.16 or later.)

       This  index  is  needed  when region arguments are used to limit samtools view and similar
       commands to particular regions of interest.

       When only one alignment file is being indexed, the output index filename can be  specified
       via -o or as shown in the second synopsis.

       When  no  output filename is specified, 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.

       -M      Interpret all filename arguments as alignment files to  be  indexed  individually.
               (Without  -M,  filename  arguments  are  interpreted  solely  as  per  the  second
               synopsis.)

       -o FILE Write the output index to FILE.  (Currently may only  be  used  when  exactly  one
               alignment file is being indexed.)

       -@, --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/>