Hi everyone, I ran Mutect2 (joint calling mode) for a set of Tumor-only samples, where for each individual I have two samples (i.e. like tumor and relapse). In the samplesheet I defined each pair as patient1,XX,1,tumor_sample,lane_1,test1_L001.bam patient1,XX,1,relapse_sample,lane_1,test2_L001.bam This results in one directory each patient with a two-samples VCF (i.e. tumor_sample and relapse_sample), exactly like in a paired Tumor-Normal run. Is this the expected behavior ? Thanks