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freeseek / mocha

MOsaic CHromosomal Alterations (MoChA) caller
MIT License
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question about calling CNV with tumor and normal-pair sample #28

Closed lizhan96 closed 1 year ago

lizhan96 commented 2 years ago

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!

freeseek commented 2 years ago

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.

lizhan96 commented 2 years ago

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

freeseek commented 2 years ago

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