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odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
61 stars 9 forks source link

phase_common is removing all variants #29

Closed williamscole closed 1 year ago

williamscole commented 1 year ago

Hello– I'm running phase_common and it is removing all my sites (says that they are multi-allelic) and then exits because there are no variants to phase. This is commit 5cc58e4 (4 Apr 2023). I also have phase_common from commit 1d357ac (2 Feb 2023) compiled and it successfully phases the same vcf. Any idea what's going on here?

Edit: I saw another post with the same problem where you had them post the output of bcftools view -G -H [vcf]. Here are the first few lines of that output (and I can attach the whole file if needed)

image
odelaneau commented 1 year ago

Hi,

Could you check if the v5.1.1 pre-release fixes your problem?

Best

williamscole commented 1 year ago

Sorry for the delayed response. Everything works perfectly now. Thanks!