FreeBayes not standard haplotype calling

[francicco]

Dear,

It's the first time I'm trying to perform this type of analysis, and I'm not in a standard situation. Here's what I have.

I have a:
- Metagenome reference. Each contig of the reference is a haploid genome
- All samples were pooled together and subsequently sequenced with MiSeq partially overlapping reads (˜80%). Each read is 300bp.

What I did:
I mapped those reads without merging them onto the reference.

I'd like to:
Call for haplotype in order to estimate the divergence of lineages for each contig of the reference.

In order to do that I'm trying to use freebayes, but I don't know exactly which parameters I do have to set. For example, I know the genomes are haploid but I don't know how many individuals I have in the pooled sample, so I'd like to call as many variants as freebayes is able to call, definitely not only the biallelic once.

Any advice?

Thanks a lot
F