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

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?

sequence cnvkit
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updated by Matteo Schiavinato Matteo Schiavinato • written by leandro.bispo.oliveira • leandro.bispo.oliveira

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.

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written by arta arta

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

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written by h.mon h.mon

2 answers

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.

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written by h.mon h.mon

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

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

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written by Matteo Schiavinato Matteo Schiavinato

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