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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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Using canvas for specific case #114

Closed beginner984 closed 5 years ago

beginner984 commented 5 years ago

Sorry This is not your issue

please help me

I have tumour and its derived model (organoid) from two patients, I want to know if there is any agreement between mutations of tumour and its derived model (organoid) but I don't have access to normal (matched or non matched samples). I want to call somatic copy numbers though. Could you please give me a hand in getting intuition to what to do in such situation? Can I still perform analysis without normal sample? If no can I use non matched normal samples in freezer ?

Thanks a lot in advance

eroller commented 5 years ago

You can still perform the analysis by using dbsnp VCF instead of the matched normal small variant VCF. Performance will likely not be as good, but the analysis should still be valid. Please check command line help for the exact options to pass.