CNV detection for amplicon sequence datas without bed file
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4 months ago
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Hello,

I want to detect CNV from normal and tumor amplicon-based samples. I tried to use two of the tools (cnvkit, covcopcan) but it didn't give a good result because I don't have a target bed file. I would be appreciated if you recommend me any tools to find CNV without using a bed file or ways to create a target bed file.

BED cnv cnvkit • 467 views
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I don't have a target bed file

well.. isn't it the real problem ?

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Unfortunately it is :(. That is why i asked here to find a solution.

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You can re-create a bed file yourself. It is quite commonly done. Identify regions well covered in both samples, divide them into parts, I don't remember exactly how long amplicons usually are but maybe around 80bp.

For amplicons it can be done actually quite accurately due to the PCR-based nature of the amplification - start/end of the amplicon should have straight peaks of reads starting exactly there.

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Thank you for your answer. I will try this with using bedtools genomecov.

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