Use HaplotypeCaller calls QC metrics

[maxulysse]

Issue by @szilvajuhos, moved from https://github.com/SciLifeLab/Sarek/issues/205

In the HaplotypeCaller calls we can check the common SNPs whether the two are the same: it can serve as a QC metric, i.e.to make sure the patients are not mixed up

[szilvajuhos]

On the long term we need a system to show whether two samples are mixed up or not. Now we have a normal-tumor-relapse case (all with matching blood) where we think the relapse belongs to someone else or the initial tumor was mixed up.