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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
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Indel, CNV and Structural Variation (SV) in Shapeit4 phasing analysis #81

Open Shicheng-Guo opened 1 year ago

Shicheng-Guo commented 1 year ago

Dear Olivier,

I am wondering how well it is for Shapeit 4 to handle INDEL, CNV, STR and SV?

Thanks.

Shicheng

klmartinez commented 1 year ago

I also have the same question.

It seems like this paper suggests that it can paired with WHATSHAP.

odelaneau commented 1 year ago

As soon as it is bi-allelic, it is treated like SNPs.

Best,

O