Trio haplotype information in the 1000 Genome Project
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12 days ago
Jesper • 0

Hi all,

I just started a new project where I am working with human genomic data for the first time, and I'm trying to understand a few things.

The 1000 Genome Project have sequenced a large number of parent-offspring trios, all of which have been phased. I am looking at some offspring and need to know what part of their parents chromosomes that they've inherited (i.e. local ancestry inference of the offspring with the parental haplotypes as sources). Is this information available somewhere, and if not, what is the best way to get to it?

I've been looking at software for phasing, but most of those seem a bit overkill and like they're designed for more complicated scenarios. I can also hack together some script of my own, but this seems like a really simple problem and something that people do all the time, so there should be some best practices for it.

Any ideas?

pedigree phasing haplotypes trio human • 96 views
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Entering edit mode
12 days ago
4galaxy77 ▴ 510

If you have the samples in a .vcf then you can use hap-ibd to detect regions of IBD between the offspring and parents.

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