Is there anyone here, maybe from the plant world, who frequently does bulk segregant analysis? I have been for the last year or so, and I am wondering if it is worth proposing a nf-core workflow. There isn't a great end analysis tool -- that has been part of the project I've been on -- and there isn't much consensus in the literature that I'm familiar with around how to generate the counts, especially in haploid or ploidy > 2 organisms. If anyone does BSA, or has done BSA, I'd be curious to know your thoughts about the value of a workflow.

There aren't many people in this channel (only 61), so you might be better off posting this in somewhere like #CE56GDKN0 where it'll get more eyes 🙂

probably true...though im still thinking about whether I even want to ask this question. It would also mean that I'd have to change what I'm currently doing, which is probably not optimal, but no one is complaining about.

I did a BSA…once? Does that count?

ha -- yes. how did you get the pileup? From something like haplotypecaller/freebayes, or directly from the pileup? Did you use a package for the analysis? Do you think it would be worth effort to turn a personal workflow into a nf-core workflow?

To be honest I had no idea what I was doing. Pretty sure I used bwa into freebayes and then filtered afterwards. Didn’t work very well but I think that was samples. Honestly, why not? It’s a specific analysis, it can reuse components from Sarek but is arguably distinct enough to warrant its own pipeline.

I inherited a workflow that does what you described above. Each new experiment included the parent strain samples so that all pooled samples would have data reported over the sites where the parents differ from the reference genome, and variants were called jointly. But, I'm thinking now (hence putting this in the rubber duck channel) that the 'active loci' could just be provided to sarek, and then the pool samples called individually. I believe that solves the ploidy with regards to the reported AD/DP issue that Ive been having.