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FreeBayes not standard haplotype calling
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
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