shapeit5 SER_phase

I performed phasing for mom-child duos (N=2326) using phase_common. After the switch step, I calculated the Switch Error Rate (SER) and found it to be around 0.51-0.91 across chromosomes 1-22. Could the high SER be due to using duos instead of trios? Are there any suggestions on how to reduce the error rate?

Mar 18 '25 16:03 elzadgeorge

How to calculate Switch Error Rate？ Thank you

Apr 22 '25 11:04 sususu-halo

I followed the steps from the tutorial: "https://odelaneau.github.io/shapeit5/docs/documentation/switch/"

Apr 22 '25 13:04 elzadgeorge

Thank you very much！

---- Replied Message ---- | From | @.> | | Date | 04/22/2025 21:43 | | To | @.> | | Cc | @.>@.> | | Subject | Re: [odelaneau/shapeit5] SER_phase_common (Issue #118) |

I followed the steps from the tutorial: "https://odelaneau.github.io/shapeit5/docs/documentation/switch/"

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elzadgeorge left a comment (odelaneau/shapeit5#118)

I followed the steps from the tutorial: "https://odelaneau.github.io/shapeit5/docs/documentation/switch/"

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Apr 22 '25 13:04 sususu-halo