Hi all! thank you for developing this pipeline, it has been very useful. I was wondering if there is a way to get a a mergerd vcf of all samples. I know it is a very simple action to perform with bcftools, but as filtered outputs are vcf and not gvcf, then reference calls will appear as "./.". Maybe there is a way to merge gvcf before and then to apply the filters. Have you thought about that?

This is not supported by the pipeline, but could maybe be a nice feature. You can however tell the pipeline to generate GVCF files instead of VCFS with `--generate_gvcf`: https://nf-co.re/rnavar/1.2.2/parameters/#generate_gvcf

Yes! thank you

@Mylena Santander I was facing same issue and I used generate gvcf to get gVcfs files first. And then I used gatk's combineGVCF function followed by GenotypeGVCFs function to get first multisampke gvcf followed by multisampke vcf file with reference depth etc included and not present as ./.

Thank you Amnah!