It is possible to make "known indels" and "dbsnp" databases optional in this pipeline as was done in Sarek?

[Jokendo-collab]

Description of feature

I am working with zebrafish genome and it lacks "known indels" and "dbsnp" databases and I see it is a mandatory requirement in this pipeline. How can one call variants from an organism lacking the above mentioned files?

[bounlu]

Maybe you can provide a dummy empty VCF file for now to trick the pipeline?

[Jokendo-collab]

Not sure if that can work but I will give it a try

[bounlu]

It should work since that VCF will be used to substract the SNPs/indels only. So x - 0 = x meaning that you will get out back what goes in. Need to test to see how that will work though.