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?