I use GATK 4.0 for the variant calling pipeline. my steps involve MarkDuplicates, BaseRecalibration, ApplyBaseRecalibration and HaplotypeCaller. When I check in a loci there is no mutation in the original BAM file in IGV, but there is a mutation in final VCF and when I check the bamout of the HaplotypeCaller there seems to be a mutation. Then I tried Sanger sequencing and see that there is actually no mutation. So the original Bam file is the right one and bamout is the wrong mutation.
So how could I overcome this problem? This is a serious issue and occurs several times. Thanks in advance.