Do VQSR for HaplotypeCaller calls

[malinlarsson]

Expected Behavior

Filter the calls from HaplotypeCaller with Variant Quality Score Recalibration according to GATK best practise (Tools VariantRecalibrator, ApplyRecalibration, see https://gatkforums.broadinstitute.org/gatk/discussion/39/variant-quality-score-recalibration-vqsr or a more recent version)

Current Behavior

Variant quality score recalibration currently not included.

[szilvajuhos]

We should do it for/with GATK 4.0 only.

[malinlarsson]

Sounds like a good plan.

[maxulysse]

Filter HaplotypeCaller variants

[apeltzer]

Keep in mind, that you'd need a "bit" of data for doing VQSR properly. The recommendation was to use at least 30 WES or 1WGS sample for performing VQSR.

I started working on a solution (in NGI-ExoSeq) to automatically download 35 of the 1000G Exome Datasets, run HaplotypeCaller on them and use them for analysis procedures with less than the minimum required 30 WES samples.

[maxulysse]

Transferred to the new nf-core/sarek repo