How To Phase Haplotypes In A Highly Polymorphic Genome

Question

[Adrian Pelin]

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.

[Istvan Albert]

What type of data do you have or plan to obtain?

[Adrian Pelin]

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.

[Istvan Albert]

Now my recommendation is to open a new question titled: "How does the samtools phase operation work?"

[Adrian Pelin]

thank you, done.

Answer 1

[Istvan Albert]

There is a writeup on the algorithms and methodologies for Haplotype Phasing here

http://cseweb.ucsd.edu/~chl107/docs/lo_research_exam.pdf

[Adrian Pelin]

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?