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Published 20 hours ago • verified publisher icon freeseek

question about calling CNV with tumor and normal-pair sample

Open lizhan96 opened this issue 2 years ago • 3 comments

Dear developer

I want to call CNV with my tumor sample(array data), and the normal-pair sample i had.

When I run the MoChA pipeline, some hg19/hg39 related files was needed.

Should I use the nomal sample related files as the input instead of that hg19/hg39 related files? Could you tell me which files I should change?

Thank you!

lizhan96 avatar May 18 '22 14:05 lizhan96

MoChA does not have a framework to compare normal and tumor data. You can analyze the two together, but they will be called as separate samples. The GRCh37/GRCh38 resources are needed for other aspects of the analyses such as phasing and knowledge of the location of common copy number polymorphisms.

freeseek avatar May 18 '22 14:05 freeseek

If I want to get the tumor somatic CNV, could you give me some suggestions to process the result of the separate sample?

lizhan96 avatar May 19 '22 01:05 lizhan96

I am not sure what I would suggest you beyond what is already in the documentation.

freeseek avatar May 19 '22 03:05 freeseek