Multi-Ancestry Phasing - best practices
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8 days ago
mari.lynne • 0

I have multi-ancestry whole genome sequence data: 2134 samples; African American = 1103; Hispanic = 153; European American = 878. Previously our group phased the data (inc some of these samples) using Eagle, however they didn't include a reference genome, but this was part of a much larger study ~10K samples.

Given the unbalanced ancestral backgrounds of my samples... is it best to phase them separated by ancestral group, and use a filtered 1000G reference panel to match? However doing this I would lose sample size in the Hispanic population. Or should I keep them all together?

Lastly, for computational efficiency can I split my data up into chromosome chunks (as is performed on the TopMed server with Eagle)?

Any recommendations much appreciated!

GWAS wgs genetics phasing • 116 views

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