I have tried using both Mutect2 and HaplotypeCaller (GATK) for calling somatic variants and generating VCF file from an aligned BAM file (RNA-seq). However, the generated VCF file did not have any information other than the header. I have seen this type of thread online, but I did not manage to find a solution. Is this because Base Recalibration was not done on the BAM file?
Meanwhile, when I try to use samtools mpileup on the same BAM file, the process aborts after a long time and it generates a VCF file of around 45GB.