Joint Discovery merge with main script

[apeltzer]

In case we dont have > 30 exomes, we could simply set up the VQSR recalibration step to take 30 exome samples from 1000G and use these as calibration samples. For bigger clusters, we could even store these without having to process them every time we analyse a single exome sample.

What do you think @marchoeppner ?

[apeltzer]

That would allow us to merge the jointdiscovery workflow again within a single script, making the entire process less annoying ...

[marchoeppner]

I would support this; we currently use in-house calbration exomes for this - we would need to make sure that we don't introduce any biases if different sequencing platforms (patterned vs non-patterned flow cells) are used (?)