Hello, I am working on a dataset of multiple polyploid individuals, all with the same ploidy (= 3). I am interested in obtaining phase information for the variants called from the sequence data.
I am just starting to work with FreeBayes after trying to use GATK UnifiedGenotyper and phasing with other programs (polyHap and HapCompass) which gave less than satisfactory results.
It is my understanding that FreeBayes uses haplotype information to make variant calls from a set of individuals. Is it possible to retrieve phase information of these variant calls? I tried running FreeBayes, but the resulting solution VCF has unphased genotypes in the GT field ("/" instead of "|").
I have a list of possible haplotypes that I could input into the analysis if needed. The following two posts would suggest phasing of multisomic variants from FreeBayes is possible:
Any help or advice would be greatly appreciated.