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 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?
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?