EAF in STITCH output

[Sajal Sthapit]

Hi Dr. Davies,

Can you point me to a resource that describes how the EAF (Estimated Allele Frequency in the INFO field) in the STITCH output vcf is calculated? Thank you.

Sajal

[Robbie Davies]

Hi,

Not sure if I've written one up. 

The EAF is calculated as the sum across all samples of the posterior distribution of the number of alternative alleles that sample has. In other words, the average of the dosage (DS) value across all samples.

Best,

Robbie

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