CNV tools for WGS data

Question

[omicj]

Hi all,

I am testing few CNV tools for WGS dataset (short reads Illumina). Few tools working on: GenomeStrip, cn.mops, Delly, ERDS, Lumpy, Ulysses. Do you have any suggestion further?

Thanks
Kevin

[Chirag Nepal]

There are multiple tools, i used varscan2/GISTIC. I wrote a tutorial here: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.

Answer 1

[Eric T.]

CNVnator and cn.MOPS are good starting points. Also look at Pindel to find smaller duplications and deletions.

If you're able to run multiple callers, consider using MetaSV to consolidate the results from all callers. This will improve your accuracy at all scales and simplify the rest of your analysis by combining the calls into a single VCF.

[rse]

Thank you Etal

CNVnator gives an error : "Too many arguments".