Question: How to call CNV without normal samples
gravatar for leovam173
14 days ago by
leovam1730 wrote:


I wonder if it is possible to detect somatic copy number variation without normal samples? As far as I can remember is that most of the tools take into the normal.BAM and tumor.BAM and they compare the read count for the targeted region and that ratio can be used to infer CNV. However, if there's no normal.BAM at all, is it still possible to call CNV from the tumor.BAM? Thanks!

sequencing cnv • 80 views
ADD COMMENTlink modified 14 days ago by abedkurdi1030 • written 14 days ago by leovam1730

There is no straightforward way to answer this but often I have seen Panel of Normals (PON) being used for such. Check this thread from Kevin Blighe. Might be of help. Copy number events can be called from the data but somatic without a reference is always tricky.

ADD REPLYlink written 14 days ago by ivivek_ngs5.0k
gravatar for abedkurdi10
14 days ago by
abedkurdi1030 wrote:

You can use cnvkit tool to call somatic CNVs. Don't forget to use --drop-low-coverage argument too.

ADD COMMENTlink written 14 days ago by abedkurdi1030
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