Pool-Seq same as normal variant calling?

Question

[andrebolerbarros]

Hello everyone,

I have some data for Pool Seq and just wanted to check if the same pipeline/approaches of Variant Calling can and should be used for Pool Seq data. I'm talking about QC filtering (fastp & contaminant filtering), alignment, duplication removal, etc.

Thanks in advance!!

[dthorbur]

From the few times I've used pool-seq data, I've processed most data in the same manner as any other variant calling. It's mostly the variant calling itself where assumptions about number of alleles becomes problematic. Though it's been a few years, so hopefully someone with more recent experience can also comment.