I have run bam files in GATK Mutect2 in "Tumor with matched normal mode" (Tumor+Normal sample) and also in "Tumor only mode" and I have also run them with and without PoN and germline resource file. Whatever I do, running vcftools afterwards for Site Quality check always returns with the value -1 (Negative 1) for each and every single position. What might I be doing wrong? Please help.
what is the vcftools command line ?