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nf-core / raredisease

Call and score variants from WGS/WES of rare disease patients.
https://nf-co.re/raredisease
MIT License
90 stars 34 forks source link

Option to publish GVCFs #602

Open sitems opened 3 months ago

sitems commented 3 months ago

Description of feature

Is it possible to publish GVCF file for every sample?

asp8200 commented 3 months ago

I'd guess it is just a matter of adjusting some so publishDir and saveAs options in some configs for the relevant variant-callers. (You might even be able to do that in a custom-config for those variant-callers.) Which variant-callers are you using the generate the gvcf-files?

sitems commented 3 months ago

Cool, I'm using deep variant with custom config. If you could help me how to modify the config, that would be great.