name: samtools index description: index a BAM or CRAM file keywords: - index tools: - samtools: description: | SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 input: - - input: type: file description: Input BAM or CRAM file pattern: *.{bam,cram} output: - - index: type: file description: BAM or CRAM index file pattern: *.{bai} authors: - @ewels