Hi
I have performed the CNVkit on WGS deduplicated bam files ( normal and tumor) using the "batch" command, I have two questions :
1- How can I find the genes with CNV ? ( I mean on which files the information could be fetch?)
2- Is the batch command for such CNV analysis ( normal bam file and tumor bam file) ?
thanks.
CNVkit can give out various tables/reports: https://cnvkit.readthedocs.io/en/stable/reports.html. For seeing which genes have CNV's and their copy-number value, you can use CNVkit's genemetrics command (https://cnvkit.readthedocs.io/en/stable/reports.html#genemetrics) which outputs a list of genes who's log2 threshold has passed a certain value (by default this is 0.2; from the page: "A threshold of .2 (the default) will report single-copy gains and losses in a completely pure tumor sample (or germline CNVs)"). If you want copy-numbers in the output, make sure cnvkit.py call has already been performed on the necessary files, otherwise only log2 (and some other columns) will be reported.
Thanks DGTool for answer. For running call you mean I need to run the call part on .cnn/.cns files again? Becuase the batch run "call" as a part of pipeline.
Ah, if it already has run call, then that should be fine, you can just run genemetrics on it and it should give you the copy-number in the output. (To check if call had run successfully on the cns/cnr files, the .cnr and/or .cns file should have a cn column in them; if yes then all good, otherwise one can run call on them separately)
Thanks a lot, How can I find the CN-LOH from those files?
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