Prints alignments in the specified input alignment file.

Usage: samtools index [-bc] [-m INT] <in.bam> aln.bam|aln.cram
-b Generate BAI-format index for BAM files [default]
-c Generate CSI-format index for BAM files
-m INT Set minimum interval size for CSI indices to 2^INT [14]

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.

This is a companion discussion topic for the original entry at quay.io/cancercollaboratory/dockstore-tool-samtools-index