Add possibility to run HaplotypeCaller without dbsnp

[maxulysse]

nf-core/sarek pull request

• Add possibility to run HaplotypeCaller without dbsnp to build a set of known sites
• cf https://gatkforums.broadinstitute.org/gatk/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x

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[maxulysse]

With @mahesh-panchal we're helping out a user with 96 samples of a species with only a ref genome to start with.
So the idea is actually to use Sarek to build a set of known sites.
I think that Strelka and HaplotypeCaller would be enough to generate a set of VCFs that can be filtered/merged and then used until convergence.

[ggabernet]

Looks good :)