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

nf-core / rnavar

gatk4 RNA variant calling pipeline

https://nf-co.re/rnavar

MIT License

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It is possible to make "known indels" and "dbsnp" databases optional in this pipeline as was done in Sarek? #118

Open Jokendo-collab opened 9 months ago

Jokendo-collab commented 9 months ago

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 commented 9 months ago

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

Jokendo-collab commented 9 months ago

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

bounlu commented 9 months ago

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.