input to pyclone-vi

[jsha129]

trafficstars

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...

-- 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 https://github.com/polyactis/Accucopy/issues/21, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAF7C2I5AVGMVTD4A3PA6VDWHM5RXANCNFSM6AAAAAAR3CD76U . You are receiving this because you are subscribed to this thread.Message ID: @.***>