Add an option to optionally use the GATK VariantFiltration instead of VQSR

[cmatKhan]

Description of feature

For haplotypecaller, if known snps or indels are not passed, then VQSR can't be used.

VQSR should be set by default. But, the user should be able to select VariantFiltration if they would rather set filter thresholds explicitly. If known snps or indels are not passed in, and haplotypecaller is selected, then VariantFiltration should be used automatically.

https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering#2

[Ons14]

Hello,

Thank you for bringing this up. I am currently working on germline variants, and it would be great if the VariantFiltration feature could be added to the Sarek pipeline.