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odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
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Phasing small sample sizes #85

Open sihaybo opened 6 months ago

sihaybo commented 6 months ago

Hi,

I am trying to phase 21 individuals with shapeit5 but I get the error "Less than 50 samples is not enough to get reliable phasing, consider using a reference panel to increase sample size". I was able to phase the same file with shapeit4, but now it is not working. I am using the static version of 5.1.1.

There is no reference panel for the organisms I am working on and sadly I also do not count with more samples. Do I still need to try to create a reference panel or is there a way around this?

Thank you very much in advance,

Sofia

srubinacci commented 6 months ago

Hi Sofia. For just 21 individuals, you can just go ahead with SHAPEIT4. You won't need to use the advanced functionalities of SHAPEIT5 to handle large amount of samples. SHAPEIT5 phase_common is basically the same algorithm as SHAPEIT4.

Best,

Simone

sihaybo commented 5 months ago

Hi Simone, Thank you so much for your reply, it is very helpful. I moved to a new cluster and I have not been able to install SHAPEIT4 via conda or compile it. Is there a way to download the SHAPEIT4 static file? I did not find it in the github page.

Thank you again.

Best,

Sofia

cjjinfinity commented 1 week ago

can you suggest a standard protocol for this in shapeit5.1