It's both a file format that stores genetic variation and the tool to work with it. Compared to VCF, it is much more compact and faster to work with. It also remembers which of the sites that didn't show a variant were called at all, allowing for a clean workflow.
Heffalump imports common file formats (VCF, BCF, Bam (by picking from an arbitrary read at each site), HETFA (the files used by SGDP), Emf and Maf), storing one file per sample. Conversely, it merges multiple heffalump files and exports them into common formats (VCF, Eigenstrat, Treemix) or computes simple statistics on it.
- install GHC (see http://haskell.org/ghc) or have your admin install it,
- run
cabal update(takes a while to download the current package list), - run
cabal install https://bitbucket.org/ustenzel/heffalump/get/master.tar.gz
If you prefer stack, instead
- run
stack build