search

nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
34 stars 31 forks source link

Add samtools mpileup as an alternative variant caller #110

Open Leon-Bichmann opened 10 months ago

Leon-Bichmann commented 10 months ago

Description of feature

I tried using the default variants called using GATK but they didn't seem to work as well for my purpose. On the contrary samtools mpileup worked extremely well.

Maybe it would be worthwhile adding it as an alternative calling procedure to this?