CNV calls from DNA read counts

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2.1 years ago

Roy ▴ 10

Hello all,

I am wanting to create a Copy number Variation frequency plot similar to the one shown below for my NGS data. I used featurecounts to get the read counts of my BAM file, but from what I know, read counts do not equal copy number. Is there a way to normalize this so I can use this for downstream analysis? I do not have a control (unless I can use other cancer samples I have) so not sure how to go about this.

If this is possible, do people recommend GISTIC, CNVkit, etc? I have not researched further as I do not have the required copy number calls yet.

Copy number freq graph example

Thanks!

ngs readcounts cnv plot • 406 views

ADD COMMENT • link updated 2.1 years ago by Ram 43k • written 2.1 years ago by Roy ▴ 10

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That looks like a plot generated from GISTIC2.0 output. Once you get the CN segment data, GISTIC2.0 should give you a bunch of region-level outputs that you can then plot easily.

ADD REPLY • link 2.1 years ago by Ram 43k

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