Hello,
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?
Thank you.
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.
•
written
by
Adrian Pelin
There is a writeup on the algorithms and methodologies for Haplotype Phasing here
I guess I should have mentioned that I have NGS data for the whole genome, and that's how I do my calls.
Does that review talk about doing it from reads?
moved to main question under edit.
don't add this as an answer though, edit your main question or add it as a comment
Log in to answer this question.
What type of data do you have or plan to obtain?
I am trying to obtain haplotypes that are phased to see how my variants are linked with each other.
I am also trying to obtain haplotype frequencies.
Now my recommendation is to open a new question titled: "How does the samtools phase operation work?"
thank you, done.