Enable joint variant calling for germline samples

[ikeller]

Allow calling of germline short variants jointly on multiple samples as outlined here https://software.broadinstitute.org/gatk/documentation/article?id=11019. This approach is expected to increase accuracy and sensitivity as it makes use of population-wide information.

Each sample is first called individually using HaplotypeCaller in -ERC GVCF mode. GenotypeGVCF is then run on all g.vcfs together. See GATK documentation here: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145

[maxulysse]

from @jfnavarro on #185

It would be nice if Sarek would support to perform a joint analysis, for example with Strelka2 and HaplotypeCaller since they both support it. It would also be nice to combine variants for each caller (all samples).

[knokknok]

Hi, any progress on this?
Thanks!

[maxulysse]

Hi @knokknok
No progress on it yet, but hopefully will start working on it soon-ish now that there is modules for both these tools nf-core/modules.
Plan is to make a sub-workflow dedicated to that (Joint variant calling).

[georgiesamaha]

Hi all, has any progress been made on this since the Hackathon in October 2021?

[FriederikeHanssen]

@GCJMackenzie is working on it at the moment to add it to 3.0

[FriederikeHanssen]

added in #595