how to extract only exon from copynumber called by Varscan2?

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5.6 years ago

9521ljh ▴ 50

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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sequence sequencing next-gen SNP • 1.3k views

ADD COMMENT • link 5.6 years ago by 9521ljh ▴ 50

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Can you show us some results/ illustrations ?

ADD REPLY • link 5.6 years ago by Titus ▴ 910

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oh sorry, i post my result of CBS by DNAcopy!

ADD REPLY • link 5.6 years ago by 9521ljh ▴ 50

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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/)

ADD REPLY • link 5.6 years ago by Titus ▴ 910

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