freebayes with pools of different number of individuals

Question

[Jeanlain]

Hi,

I'd like to use freebayes for SNP calling on poolseq data, but I have pools of different sizes. Some have 30 individuals, some have 24, others 26.

The -p argument to set ploidy (here, pool size) is fixed. I'd rather not do separate SNP callings on the pools just so I could set a different -p for each.

Can I use the --cnv-map argument to specify the pool sizes? Or should I just set -p 60, even if some pools have fewer than 30 indviduals?

Should I consider CRISP caller instead of freebayes? It's designed for poolseq, but it seems rather old.

I any case, I'd rather not simply do a mpileup to feed to popoolation as mpileup seems too basic (not really a SNP caller, it may make errors due to read alignment errors I suppose).

Thanks.

Jean