I have list of regions ( chr:start-end) for which I would like to build two consensus haplotypes. I could not use the FastaAlternateReferenceMaker from GATK and it ignores the phasing information with in the region of interest. My question is more detailed in this image:
I could try GATK HaplotypeCaller but I have already called SNPs using freebayes and would like to know if there is any existing method/tool to do this. There are tools that constructs haplotypes but they look complicated and are for different purpose. I am looking for something simple. Otherwise I will end up writing a dirty script, which may not work in all possible scenarios.