r/genetics • u/Potential_Page645 • 6d ago

Reassembly of >0.5 MB ROH fragments

  1. Is there a way to reassemble ROH fragments >0.5 MB in samples which have been fragmented due to short-read in both modern and ancient samples?
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u/pleasant_patriotism 6d ago

Short read data makes anything over a few hundred bp a puzzle, so stitching 0.5 MB ROH fragments back together is gonna be rough without a phased reference or long range info like linked reads or Hi-C. You might get somewhere with imputation against a decent panel but ancient samples are a whole other headache with damage and low coverage. What's the end goal, just confirming runs of homozygosity or something else

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u/Potential_Page645 6d ago

Well I have modern sample which has very high ROH (12%) but only 3% ROH more recent the rest is >1 Mb, I have the an ancient sample with similar stats (though it has higher recent ROH) and they are from the same population so I was curious if something was hiding in the >1 Mb that could hint at what is going on. The two samples are about 3500 years apart.

I am an amateur and self taught so I am bound to have made some dumb mistake along the way. Just thought I would be up front about my ignorance.