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
- 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].
Written by Heng Li from the Sanger Institute.
samtools(1),
samtools-idxstats(1),
samtools-view(1)
Samtools website: <
http://www.htslib.org/>