What parameters should be used for unknown number of samples in a pool?

[vibansal]

What parameters should be used for unknown number of samples in a pool?

[vibansal]

That depends on the lowest allele frequency that one would like to detect. With Illumina sequencing, variants with 2% allele frequency (pool size = 50) or even lower should be detectable with high accuracy.

[Buuntu]

Okay, so the pool size can be thought of as what allele frequency you want to select for? So even though the pool size might be in the 1000s, if we want an allele frequency of say 25%, we would just set the pool size to 4?

[vibansal]

CRISP is designed for pools with discrete number of alleles or chromosomes. The pool size determines the minimum allele frequency that is expected at a variant position.

[Buuntu]

So for an unknown number of alleles (monoploid organism), since we don't know how many organisms are in the pool, it may not be the right tool?

[vibansal]

It can work for the non-discrete model as well. There are other tools such as freebayes or lofreq that allow for continuous allele frequencies.