Support for merged output

[mylena-s]

Description of feature

Request: option to output a merged VCF with reference calls preserved

I would like to request a feature to generate a merged VCF across all samples with reference calls retained.

Currently, merging sample vcfs would require downstream merging of raw gvcf and applying filtering after that.

A potential solution would be to allow merging at the GVCF stage prior to filtering, followed by application of the existing filters.

Would it be feasible to add an option to support merging GVCFs before filtering?

Thank you for developing this pipeline!

[amnahsiddiqa]

I think this is pretty feasible since we just need to add two more commands from GATK workflow. After running nf-core/ranvar pipeline with --generate gVCF flag I used the gVCF files as input to GATK's functions CombineGVCFs and Genotype GVCFs (attached screenshots). I would see if I can help with this feature request.