deletions and double mutations in VCF file seem causing problem

[jeffchen2000]

Hi Amkozlov

#CHROM POS ID REF ALT
13 32915031 . TG CG,T
13 32915410 . CAATT C

cellphy report format error at the above two lines in my VCF file, the "TG" and "CAATT" cause format issue. any comments please?

thanks
Jeff C

[dapogon]

Hi Jeff, CellPhy works only with SNVs. Best, D

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On Wed, Oct 12, 2022, 18:55 jeffchen2000 ***@***.***> wrote: Hi Amkozlov #CHROM POS ID REF ALT 13 32915031 . TG CG,T 13 32915410 . CAATT C cellphy report format error at the above two lines in my VCF file, any comments please? thanks Jeff C — Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE4VEEVXJH5VHUV4DJGPX5TWC3URPANCNFSM6AAAAAARDPIUPY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jeffchen2000]

hi Dapogon
thanks for quick response!
since I also find this format in my VCF file and seems cellphy does not complain about this format
chr17 41203093 . G *,A

so can I change (this deletion)
13 32915410 . CAATT C
to (a SNV) like below?
13 32915410 . C *,C

sorry asking about this question, because that deletion is very important to us, we cannot skip it!

thanks for any comments.
Jeff C

[dapogon]

Not sure what is going to do with that... Alexey? You can indeed code any event as a fake snv, but this has potential implications on multiple parameter estimates

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On Wed, Oct 12, 2022, 21:29 jeffchen2000 ***@***.***> wrote: hi Dapogon thanks for quick response! since I also find this format in my VCF file and seems cellphy does not complain about this format chr17 41203093 . G *,A so can I change (this deletion) 13 32915410 . CAATT C to (a SNV) like below? 13 32915410 . C *,C sorry asking about this question, because that deletion is very important to us, we cannot skip it! thanks for any comments. Jeff C — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE4VEERRITWUUHTN37IKYC3WC4GRDANCNFSM6AAAAAARDPIUPY> . You are receiving this because you commented.Message ID: ***@***.***>

[jeffchen2000]

WOW! Implementing such a fake snv will be absolutely useful! Thanks in advance! Jeff C