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? My data is reads in fastq format, representing illumina NGS of the entire genome. I aligned it to a reference using bwa.
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.