1samtools-index(1)            Bioinformatics tools            samtools-index(1)
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NAME

6       samtools index - indexes SAM/BAM/CRAM files
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SYNOPSIS

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

13       Index  a  coordinate-sorted  BGZIP-compressed SAM, BAM or CRAM file for
14       fast random access.  Note for SAM this only works if the file has  been
15       BGZF compressed first.
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17       This  index  is needed when region arguments are used to limit samtools
18       view and similar commands to particular regions of interest.
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20       If an output filename is given, the  index  file  will  be  written  to
21       out.index.    Otherwise,   for   a   CRAM  file  aln.cram,  index  file
22       aln.cram.crai  will  be  created;  for  a  BAM  file  aln.bam,   either
23       aln.bam.bai  or  aln.bam.csi  will be created; and for a compressed SAM
24       file aln.sam.gz, either aln.sam.gz.bai or aln.sam.gz.csi will  be  cre‐
25       ated, depending on the index format selected.
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27       The  BAI  index  format can handle individual chromosomes up to 512 Mbp
28       (2^29 bases) in length.  If your input file might contain reads  mapped
29       to positions greater than that, you will need to use a CSI index.
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OPTIONS

33       -b      Create a BAI index.  This is currently the default when no for‐
34               mat options are used.
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36       -c      Create a CSI index.  By default, the minimum interval size  for
37               the index is 2^14, which is the same as the fixed value used by
38               the BAI format.
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40       -m INT  Create a CSI index, with a minimum interval size of 2^INT.
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42       -@, --threads INT
43               Number of input/output compression threads to use  in  addition
44               to main thread [0].
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AUTHOR

48       Written by Heng Li from the Sanger Institute.
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SEE ALSO

52       samtools(1), samtools-idxstats(1), samtools-view(1)
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54       Samtools website: <http://www.htslib.org/>
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58samtools-1.13                     7 July 2021                samtools-index(1)
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