Phasing of small parent-offspring sample

odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool

https://odelaneau.github.io/shapeit5/

MIT License

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Phasing of small parent-offspring sample #82

Closed friedav closed 6 months ago

friedav commented 7 months ago

Dear SHAPEIT5 team,

for the genotype imputation (common variants) of a small sample of 133 mother-offspring duos (total n=266) from SNP array data, I am wondering if it is better to perform phasing based on

Usage2 (phasing related samples) with the --pedigree option
Usage4 (phasing using a reference panel) with the --reference option

Or is it possible (and helpful) to combine both?

Thank you for any recommendations. Best, Friederike

RJHFMSTR commented 6 months ago

Hi Friederike,

The --pedigree option allows you to have an accurate phasing of offsprings, but not mothers. Depending on your needs, I would advice to use both.

Best, Robin