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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

multi-allelic sites defaults supported？ #17

Closed octpus616 closed 1 year ago

octpus616 commented 1 year ago

Hi, Thanks for development shapeit5, I know that shapeit is a widely recognized phased software, but earlier versions of shapeit such as shapeit2 don't seem to accept multi-allelic sites. Has the lastest version of shapeit5 added this support?

Regrads Zhang

odelaneau commented 1 year ago

Nop, you should use bcftools norm before processing multi-allelic sites in order to decompose multi-allelic into a series of bi-alleleic.

Hope that helps,

Olivier Delaneau

Le lun. 3 avr. 2023 à 10:05, octpus616 @.***> a écrit :

Hi, Thanks for development shapeit5, I know that shapeit is a widely recognized phased software, but earlier versions of shapeit such as shapeit2 don't seem to accept multi-allelic sites. Has the lastest version of shapeit5 added this support?

Regrads Zhang

— Reply to this email directly, view it on GitHub https://github.com/odelaneau/shapeit5/issues/17, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD4XTIOMYMY47RCP2TMQSWLW7KAC7ANCNFSM6AAAAAAWQ6NQJ4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

octpus616 commented 1 year ago

Hi，@odelaneau Thanks for your reply, I have an additional question. The vcf may contain many lines with one same position after bcftools norm if there is a multi-allelic siites. Is shapeit5 can accpected this? or I need to do someting more?

odelaneau commented 1 year ago

S5 uses position, REF and ALT to uniquely identify variant sites. So, having multiple sites at the same position is not an issue as long as they do not share the same REF and ALT alleles.

Olivier Delaneau

Le lun. 3 avr. 2023 à 10:28, octpus616 @.***> a écrit :

@.*** https://github.com/odelaneau Thanks for your reply, I have an additional question. The vcf may contain many lines with one same position if there is a multi-allelic siites. Is shapeit5 can accpected this? or I need to do someting more?

— Reply to this email directly, view it on GitHub https://github.com/odelaneau/shapeit5/issues/17#issuecomment-1493897408, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD4XTINNRI2TCONNCMPUDZLW7KC2RANCNFSM6AAAAAAWQ6NQJ4 . You are receiving this because you were mentioned.Message ID: @.***>

octpus616 commented 1 year ago

Hi, @odelaneau Thank you for your kind help. I appreciate your time and effort in solving my problem. I have learned a lot from your explanation. You are awesome! Please allow me for having an extra question that is unrelated to this topic, so I opened another issue. I will close this issue, thank you again for your help.