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Question: Is there a way to use CNVkit without a reference from normal samples?
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gravatar for leandro.bispo.oliveira
2.8 years ago by
leandro.bispo.oliveira • 0
leandro.bispo.oliveira • 0 wrote:

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 • 1.7k views
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modified 2.8 years ago by h.mon ♦ 32k • written 2.8 years ago by leandro.bispo.oliveira • 0

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.

ADD REPLY • link written 2.8 years ago by arta • 620

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

ADD REPLY • link written 2.8 years ago by h.mon ♦ 32k
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gravatar for h.mon
2.8 years ago by
h.mon ♦ 32k
Brazil
h.mon ♦ 32k wrote:

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.
ADD COMMENT • link written 2.8 years ago by h.mon ♦ 32k
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