{"id":6249,"projects":[69],"description":"Prints alignments in the specified input alignment file.\n\nUsage: samtools index [-bc] [-m INT] <in.bam> aln.bam|aln.cram\nOptions:\n  -b       Generate BAI-format index for BAM files [default]\n  -c       Generate CSI-format index for BAM files\n  -m INT   Set minimum interval size for CSI indices to 2^INT [14]\n\nFor 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.","image":"","tags":"","type":"","title":"dockstore-tool-samtools-index","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcancercollaboratory%2Fdockstore-tool-samtools-index","authors":[1],"rubrics":[25]}