I generated two VCFs, one with freebayes and one with GATK on the same BAM file.
At one position, freebayes called an MNV. At the same position, GATK called an SNV. What confuses me is that the depths are different in the VCF file. for example,
chr 9 35906602 C A,T 0/1 6,7,6:19
and GATK called:
chr 9 35906602 C A 0/1 8,7:21
This might be obvious, but I'm new to all this. How can two callers report different total read depths like this? And how would one caller report a higher reference than the other?