Sambamba

• sambamba-flagstat(1) flagstat - getting flag statistics from BAM file
• sambamba-index(1) index - tool for building standard index files for BAM data
• sambamba-markdup(1) markdup - finding duplicate reads in BAM file
• sambamba-merge(1) merge - tool for merging several BAM files into one
• sambamba-pileup(1) mileup - make a pileup
• sambamba-slice(1) slice - copying a slice of BAM file
• sambamba-sort(1) sort - tool for sorting BAM files
• sambamba-view(1) view - tool for extracting information from SAM/BAM files
• sambamba(1) toolkit for working with SAM/BAM files