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raphael-group / decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
BSD 3-Clause "New" or "Revised" License
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Question regrading CNAs #15

Closed maxanes closed 2 years ago

maxanes commented 2 years ago

Hi, I have identified CNAs with PureCN tool, and I have these two files as output:

1, normal.alignment_coverage_loess.txt.gz (from the normal sample and the same from tumor sample of the same patient) looking like below: image

2, dnacopy.seg which is short one line for each chr looking like below: image

Can you please help me with which of these two files to use and try to make that output looks like best.seg.ucn, is it the second one?

Thank you.

simozacca commented 2 years ago

The current version of DeCiFer requires allele-specific copy number calls; this is essential for accurate tracking the multiplicities and evolution of somatic mutations. Your data only contains total copy numbers. So the use of an allele-specific copy number caller would be required.

Please let us know if you have any further question.