NAME

       sambamba - toolkit for working with SAM/BAM/CRAM files

SYNOPSIS

       sambamba [subcommand] [arguments...]

DESCRIPTION

       sambamba unifies several independent tools in one executable:

       •   sambamba-view(1)

       •   sambamba-index(1)

       •   sambamba-merge(1)

       •   sambamba-sort(1)

       •   sambamba-markdup(1)

       •   sambamba-flagstat(1)

       •   sambamba-slice(1)

       •   sambamba-pileup(1)

       Thus  available  subcommands  are  view, index, merge, sort, markdup, flagstat, slice, and
       mpileup. Their use is explained on the corresponding man pages.

       Note that sambamba uses all available cores by default.

                                          February 2015                               SAMBAMBA(1)