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I'm new to this area (but not to programming & algorithmics) and I want to help a friend to solve a problem (I don't need source code, I just want to understand the problem itself).

He needs a cycle to phase haplotypes ("I need find haplotype pattern(s) from SNP string"). He also said "The method is simple, I need to compare homozygot combinations (AA, BB) in sequence with haplotype chains. And ignore heterozygot pairs (AB) at their right positions."

An an input he has a SNP string and a bunch of haplotypes strings (array).

Any help is greatly appreciated.

Thank you!

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Rather than re-explaining the basics of haplotype phasing, I will refer you to useful documentation. One of the first works on haplotype phasing has been perfromed by Andrew Clark. You can find here a nice slide presentation detailing the problem. Useful discussion is going on here on Biostars. I suggest you to use of the several approaches that have already been developed: my favorites are Beagle and fastPHASE.

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  • $\begingroup$ Thank you. I managed to do it in PHP (really great on working with strings) $\endgroup$ – Sorin Trimbitas Aug 1 '17 at 9:46

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