which tool can I use to detect CNVs?

Question

[Elisa]

Hi everyone,

I have performed target sequencing on tumour samples (with MiSeq, Illumina). I must perform CNV detection, which tool do you suggest me to use ? (I do not have the normal samples, only tumour samples).

Thanks, Elisa

[patelk26]

You could try CNVkit. You can create a reference copy number profile without normal samples.

[Elisa]

Thank you. Does CNVkit output a VCF with all the detected CNVs and the field gain/loss?

[patelk26]

Yes, CNVkit outputs a VCF file.

Quoting from CNVkit manual: https://cnvkit.readthedocs.io/en/stable/importexport.html

Convert segments, ideally already adjusted by the call command, to a VCF file. Copy ratios are converted to absolute integers, as with BED export, and VCF records are created for the segments where the copy number is different from the expected ploidy (e.g. 2 on autosomes, 1 on haploid sex chromosomes, depending on sample sex).

[brunobsouzaa]

cnvkit and ExomeDepth are great tools for that. Also, both are pretty straightforward to use.

[Elisa]

Thank you. Does CNVkit output a VCF with all the detected CNVs and the field gain/loss?

[brunobsouzaa]

Yes... Take a look into the manual, It's very easy to follow