Using CNVkit with THetA2 and "Sample_paired.vcf"?

[ngs-seqer]

Hi,

I use the pooled and not-matched normal samples to run cnvkit and now I want to create *interval_count, *tumor.snp_formatted.txt and *normal.snp_formatted.txt to run THetA2.

I found this example in your manual:

cnvkit.py export theta Sample_T.cns reference.cnn -v Sample_Paired.vcf

I can locate *cns and reference.cnn files generated from the CNVkit-batch mode, but where is this "Sample-Paired.vcf"? or How can I generate this vcf file?

Could you provide some example codes showing how to get this vcf file?