Is there a way to use CNVkit without a reference from normal samples?

Question

[leandro.bispo.oliveira]

I am currently trying to find the CNV in some WGS data.

Is there a command to run CNVkit on a .bam data without using a Reference from Normal Samples?

[arta]

As far as i know, CNV requires reference genome. If you do not have a reference available, you can either build a de novo reference from your reads or find closest species whose reference file is available.

[h.mon]

He is not asking about a reference genome, he is asking about reference (normal) samples.

Answer 1

[h.mon]

Create a “flat” reference which assumes equal coverage in all bins by using the --normal/-n flag without specifying any additional BAM files:

cnvkit.py batch *Tumor.bam -n -t my_baits.bed -f hg19.fasta \
    --access data/access-5kb-mappable.hg19.bed \
    --output-reference my_flat_reference.cnn -d example2/

See further comments here.

Answer 2

[Matteo Schiavinato]

For future readers, here's how to do it from their documentation:

https://cnvkit.readthedocs.io/en/stable/pipeline.html#with-no-control-samples