Best way to phase regions with known recombinations?
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6.9 years ago

Hi,

I have SNP data for nuclear families with at least three children where one child has a disease and the siblings are 'normal'. Using these families, I was able to infer meiotic recombination events in the children. Subsequently, I binned these recombinations and isolated regions in the genome with an enrichment for recombination in cases compared to the sibling controls.

Using these regions, I want to explore the idea that recombinations can create novel haplotypes and so I wish to phase the SNPs in these bins.

I tried using plink but where a recombination occurs, plink fails to phase the region (returns NA). I am new to phasing and so would like to know what phasing software you would recommend and if it can handle recombinant regions.

Thanks.

Phasing Recombination Haplotypes • 1.8k views
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Entering edit mode
6.9 years ago
Adam ★ 1.0k

Sounds like you might want to try Merlin:

http://www.sph.umich.edu/csg/abecasis/Merlin/

 

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