Apply maftools based on CNS file generated by CNVkit

[xiw588]

Describe the issue Hi, I want to apply maftools to CNV data based on CNS files generated by CNVkit. Each sample has each file. Do you know if this can be easily feed into maftools?

Thank you.

Command Please post your commands and the output (errors or any unexpected output)

Session info Run sessionInfo() and post the output below

[PoisonAlien]

Hi,

I have no idea how the file looks like. Could you please provide an example file or paste few rows of the file? I would suggest you run GISTIC on all those files to identify recurrently altered CNV regions, which can then be imported into maftools.

[wangshun1121]

Aha, I have similar demand, even though my CNV caller are cnv_facets and Sequenza rather than CNVkit. I wonder if maftools can accept CNV results from sources other than GISTIC.

[PoisonAlien]

Hi @wangshun1121 , Thanks for the issue and apologies for the delay. I would love to support other tools. Could you please share few outputs from cnv_facets or Sequenza?

[wangshun1121]

Facets.zip

This is an example of Facets results. The most important file is *.vcf.gz, which gave details of every CNV region. By the way, definition of CNV types can be found at https://github.com/dariober/cnv_facets/blob/44fdd18a4beb4f57c6e6e746d31a6399efdbc85b/bin/cnv_facets.R#L563-L577

[wangshun1121]

Sequnza.zip

Here are Sequenza outputs. In this folder, *_segments.txt is most import, CNV regions' details are recorded.

[wangshun1121]

These two CNV callers are allele-specific, meaning that they can detect LOH regions without alteration of reads coverage: that's the advantage over callers depend only on coverage such as CNV-kit, and of course, GISTIC. In folders I shared, there are only results of one sample, perhaps we can use a file-list to import results of several samples into maftool.

[PoisonAlien]

Hi, Thanks for sharing. I will see what I can do. Btw, you'd like to use these results to merge with MAF and further visualizations rite? for example, oncoplot with CNV data.

[wangshun1121]

Both, if possible

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