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3.1 years ago
Elisa
•
0
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
You could try CNVkit. You can create a reference copy number profile without normal samples.
Thank you. Does CNVkit output a VCF with all the detected CNVs and the field gain/loss?
Yes, CNVkit outputs a VCF file.
Quoting from CNVkit manual: https://cnvkit.readthedocs.io/en/stable/importexport.html
cnvkit
andExomeDepth
are great tools for that. Also, both are pretty straightforward to use.Thank you. Does CNVkit output a VCF with all the detected CNVs and the field gain/loss?
Yes... Take a look into the manual, It's very easy to follow