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jpuntomarcos / CNVfilteR

R package to remove false positives of CNV calling tools by using SNV calls
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Can CNVfilteR algorithm be applied to WES data of tumor samples #6

Open HengqiLiu opened 2 years ago

HengqiLiu commented 2 years ago

Hi Jpuntomarcos: Thank you for developing the CNVfilter algorithm. I want to know whetherCNVfilteR algorithm can be applied to WES data of tumor samples. We know that for tumor samples, we need to retain somatic CNVs and filter out germline CNVs. But for the tumor-only pipline, we cannot use a tumor sample to correspond to a germline sample, which will result in many residual germline CNVs. So I want to know if this algorithm can help to remove this part of the remaining germline CNV, thereby improving the accuracy of somatic CNV results.

jpuntomarcos commented 2 years ago

Hi HengqiLiu,

CNVfilteR cannot be applied to identify false positives in somatic CNVs calls. What about residual germline CNVs in tumor samples? The problem is that somatic SNVs can also reach high allele frequency values, so usign SNVs to discard CNVs is not appropiate because we cannot easily distinguish whether a certain SNV is somatic or germline without comparing it with a germline paired sample.