Question: how to understand output form from CNVkit
0
gravatar for prosium
13 months ago by
prosium0
prosium0 wrote:

I've had 300 WGS matched samples and ran 'batch function' from CNVkit with command below.

cnvkit.py batch WGS*Tumor.bam --normal WGS*Normal.bam --annotate refFlat_hg38.txt --fasta hg38.fa --output-reference ref.cnn --output-dir results --diagram --scatter -p 20 -m wgs

output format is below

ref.cnn
WGS_01_Normal.antitargetcoverage.cnn
WGS_01_Normal.targetcoverage.cnn
WGS_02_Normal.antitargetcoverage.cnn
WGS_02_Normal.targetcoverage.cnn
...

Is it right for these output? Ultimately do I have to check CNV for tumor samples?

And then, I ran again separately with reference post C: I got a problem with making normal reference using cnvkit

cnvkit.py coverage -p 4 WGS_01_Normal.bam hg38.target.bed -o WGS_01_N.targetcoverage.cnn
cnvkit.py coverage -p 4 WGS_01_Tumor.bam hg38.target.bed -o WGS_01_T.targetcoverage.cnn

they differ the results.

I got 2 questions.

1) Is it the same betwen 'batch' and each calculation?

2) If 'batch' is right, where is tumor coverage?

Thanks.

cnvkit cnv wgs • 409 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by prosium0
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