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?
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.
He is not asking about a reference genome, he is asking about reference (normal) samples.
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.
For future readers, here's how to do it from their documentation:
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