<p>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:</p>

<p>https://www.dropbox.com/s/hkg4eff9ba8zg37/Screen%20Shot%202015-12-26%20at%2013.57.49.png?dl=0</p>

<p>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.</p>

<p>just a quick suggestion: use ReadBackedPhasing ( https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_phasing_ReadBackedPhasing.php ) to generate a VCF with the phasing information. Use this phasing to produce two VCFs for each strand, and then go back to FastaAlternateReferenceMaker ?</p>
