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amkozlov / cellphy

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies
GNU Affero General Public License v3.0
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deletions and double mutations in VCF file seem causing problem #3

Open jeffchen2000 opened 1 year ago

jeffchen2000 commented 1 year ago

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 commented 1 year ago

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

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 https://github.com/amkozlov/cellphy/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE4VEEVXJH5VHUV4DJGPX5TWC3URPANCNFSM6AAAAAARDPIUPY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

jeffchen2000 commented 1 year ago

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 commented 1 year ago

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

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 https://github.com/amkozlov/cellphy/issues/3#issuecomment-1276642595, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE4VEERRITWUUHTN37IKYC3WC4GRDANCNFSM6AAAAAARDPIUPY . You are receiving this because you commented.Message ID: @.***>

jeffchen2000 commented 1 year ago

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