GATK is slow, investigate alternatives to speed things up

[matthdsm]

Description of feature

benchmark freebayes and elprep for speed and accuracy

https://github.com/freebayes/freebayes
https://github.com/ExaScience/elprep

[nvnieuwk]

Elprep has been added to the pipeline, but is currently not maintained by the original developers. Might come back to this issue later

[matthdsm]

Deepvariant 1.8 is toted to be up to 40% faster, so maybe we need to re-evaluate

[matthdsm]

Deepvariant 1.9 is out with another 20% speed boost

[nvnieuwk]

I'll put additional tests on my TODO!