Manual page from samtools-1.20
released on 15 April 2024


samtools index – indexes SAM/BAM/CRAM files


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

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


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.


-b, --bai

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

-c, --csi

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, --min-shift INT

Create a CSI index, with a minimum interval size of 2^INT.


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

-o, --output 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].


Written by Heng Li from the Sanger Institute.


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

Samtools website: <>