input to pyclone-vi

[jsha129]

Hi there, thank you for developing accucopy. it was relatively straight forward to run and fast! How do we prepare input for pyclone-vi (example: https://github.com/Roth-Lab/pyclone-vi/blob/master/examples/tracerx.tsv) from cnv.output.tsv? Specifically, how do we get major_cn and minor_cn? I think pyclone-vi only accepts integer values for both.
Thanks

[polyactis]

Please check https://www.yfish.org/display/PUB/Accucopy#Accucopy-cnv.output.tsv cp is the total copy number. major_allele_cp is the copy number for the major allele (=major_cn of Pyclone VI?). We are not familiar with PYClone VI...

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-- Yu S. Huang http://www.yfish.org/ https://sites.google.com/site/polyactis/

On Wed, Nov 9, 2022 at 2:07 PM Jaynish Shah ***@***.***> wrote: Hi there, thank you for developing accucopy. it was relatively straight forward to run and fast! How do we prepare input for pyclone-vi (example: https://github.com/Roth-Lab/pyclone-vi/blob/master/examples/tracerx.tsv) from cnv.output.tsv? Specifically, how do we get major_cn and minor_cn? I think pyclone-vi only accepts integer values for both. Thanks — Reply to this email directly, view it on GitHub <#21>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAF7C2I5AVGMVTD4A3PA6VDWHM5RXANCNFSM6AAAAAAR3CD76U> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>