how to extract only exon from copynumber called by Varscan2?
Hi. i have tumor, normal data(DNAsequence)
i run the copy number calling by Varscan2. And then run CBS(DNAcopy of Rpacakge).
but there is so many noise on the graph. I think it is caused by all region of dna.
Therefore i want to extract only exon data from copynumber called from Varscan2.
But How??
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Can you show us some results/ illustrations ?
oh sorry, i post my result of CBS by DNAcopy!
How many samples did you comprare ? I think you should filter the ratio of CNV with the log parameter if you doesn't. You can extract you data using a bed of exome and bedtools (https://bedtools.readthedocs.io/en/latest/)