method

[stroke1989]

Hi, I'm a new to cnvkit. Thanks for this excellent tool. As it was pointed out in the documentation, CNVkit is primarily designed for use on hybrid capture sequencing data, where off-target reads are present and can be used improve copy number estimates. However, CNVkit can also be used on whole-genome sequencing (WGS) and targeted amplicon sequencing (TAS) datasets by using alternative command-line options.

The batch command supports these workflows through the -m/--method option.
My data are WES sequencing, which method should I choose？--method wgs OR --method hybrid? Hope your reponse.

[tetedange13]

Hi @stroke1989,

Contrary to WGS where you take all input DNA, Whole Exome Sequencing is part of the "enrichment methods"
=> Same as a panel of genes, except that here you are targetting all exons from all genes

Among "enrichment methods" :

• Some are PCR-based, meaning regions of interest (ROI) are amplified with specific primers
• Others are based on hybrid-capture method, which uses probes whose sequence complements your ROI

These 3 wetlab cases are reflected by --method param possible values
=> As far as I know most WES wetlabs are hybrid-capture based, so you can go with --method hybrid (which is default so no need to explicitly set this parameter)
=> But you should be able to check this information (regarding enrichment method) in your wetlab protocol

Hope this helped !
Have a nice day,
Felix.

[etal]

Answered: WES is hybrid-capture, use default hybrid. Closing as answered — please reopen, or open a new issue, if a concrete problem remains.

For general usage questions, we now use GitHub Discussions (Q&A): https://github.com/etal/cnvkit/discussions