I got somatic mutation list with MuTect2, and it is in vcf format. The last 2 columns in the vcf file are for tumor sample and normal sample for one patient.

If I input this vcf file to oncotator for annotation, oncotator perceives the last 2 columns as 2 patient, and for each row in vcf file, creates 2 rows in oncotator ouput file, 2 rows are for normal and tumor.

Previously, I was using MuTect (.maf) and Oncotator 1.8, and I did not have this problem. Now, I am using MuTect2 and Oncotator 1.9.

I want one row for one mutation in a patient. Currently there are 2 rows for one mutation in one patient, one row is for normal sample, the other row is for tumor sample. The 2 rows are almost identical, except those rows that has coverage information or sample name information. I can manually fix the output from oncotator, but is there any easy way to solve this problem?