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Question: How To Phase Haplotypes In A Highly Polymorphic Genome
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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.

ADD COMMENTlink 6.1 years ago Adrian Pelin ♦ 2.3k • updated 2.1 years ago Biostar 20
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What type of data do you have or plan to obtain?

ADD REPLYlink 6.1 years ago
Istvan Albert
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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.

ADD REPLYlink 6.1 years ago
Adrian Pelin
♦ 2.3k
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Now my recommendation is to open a new question titled: "How does the samtools phase operation work?"

ADD REPLYlink 6.1 years ago
Istvan Albert
80k
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thank you, done.

ADD REPLYlink 6.1 years ago
Adrian Pelin
♦ 2.3k
1
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There is a writeup on the algorithms and methodologies for Haplotype Phasing here

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

ADD COMMENTlink 6.1 years ago Istvan Albert 80k
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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?

ADD REPLYlink 6.1 years ago
Adrian Pelin
♦ 2.3k

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