Manual page from samtools-1.10
released on 6 December 2019


samtools index – indexes SAM/BAM/CRAM files


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


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.



Create a BAI index. This is currently the default when no format options are used.


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.


Written by Heng Li from the Sanger Institute.


samtools (1), samtools-idxstats (1), samtools-view (1)

Samtools website: <>