Hello everone! I wonder if someone could recommend some pipelines to perform bulk segregant analysis (BSA) for SNPs obtained using genotyping-by-sequencing (GBS) technology. The details of the analysis are almost completely absent in experimental articles like this so it is hard to find appropriate tool for BSA.

In my opinion in case of using GBS or RAD-seq the analysis should be pretty standard and look the following:

1) Read filtering (Trimmomatic)

2) Alignment (BWA)

3) SNP-calling (GATK)

4) bulk segregant analysis (???)

The problem is that I didn't find a tool that is broadly (like GATK or BWA) used for such studies. I stumbled upon multipool however it looks like a black box. If you faced such problem with BSA or GBS-BSA, in particular, please share your experience or paper/pipeline/tutorial.