Overview

samtools index [-bc] [-m INT] aln.bam|aln.cram [out.index] Index a coordinate-sorted BAM or CRAM file for fast random access. (Note that this does not work with SAM files even if they are bgzip compressed — to index such files, use tabix(1) instead.) 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, depending on the index format selected.

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