Hi,
I would really appreciate if anyone could provide some advice or strategies to address the following problem. We have target exome sequenced 250 patients and after processing the data (MAF <1% and annovar), we have around 270 variants with per sample containing around 8 variants and a single variant present in the samples ranging from 1 to 240. The variants present in higher number of samples have MAF < 0.01 or no MAF thus they have not been excluded from the list.
Is there a way to cluster these variants based on the patient sample it is present in to determine the causal variants? I have patient information like the type of cancer, receptor status, grade and stage?
Is there a R package to use these information to cluster the variants? Kindly provide your suggestions.
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It seems you want to link variants to cancer type. If this is the case, look for rare variant association tests in the literature.