Deletion no longer being called

[cpmorris82]

Hello,
We run positive controls from previous specimens as part of our quality control. We are running the Medaka pipeline. On the current version of Artic, there is a deletion that was called on multiple previous samples at 28271 (Alpha) (SARS-COV-2), which appears to currently be filtered out. This is a 1 nucleotide deletion that appears real on BAM files, and is present in the vcf.pass file but is not present in the ending vcf.merge file. It appears as if it is actively being filtered out. Depth in the region is good. Is this supposed to be filtered out now?
Thank you!
Paul