I have a highly polymorphic (10% polymorphism rate) genome. I expect this variation to be due to heterozygosity. What is the best way to try and phase my haplotypes?
EDIT: I found samtools has such a module called phase, and I phased my .bam file. However, I have no idea what to do with it to analyze the ouput. I wanted to be able to extract the build phased haplotypes and to measure their frequencies.