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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
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About including PS (phase set) information #42

Closed SIJAE-WOO closed 3 years ago

SIJAE-WOO commented 3 years ago

Hi, I ran shapeit4 using '--use-PS' option. But, PS (phase set) information was not included in the output file of shapeit4. image

I want to check GT (genotype) with PS (phase set), simultaneously. If you have a solution, please let me know. Otherwise, is there only one phase set in the output file (in other words, all phased variants are in the same phase set)?

Bests,

Sijae

odelaneau commented 3 years ago

Dear Sijae,

After a S4 run base don --use-PS, all variants are in the same PS, so no need to specify it in the output.

Best,

Olivier

SIJAE-WOO commented 3 years ago

I got it. Thank you very much!

Sijae