Closed octpus616 closed 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: @.***>
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?
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: @.***>
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.
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