negative control in hla locus amplification

Question

[vmicrobio]

We are testing GenDx for HLA Locus-Specific Amplification using Proton technology. The problem is that negative controls are amplified. Several control have been done and experimentation problems are excluded.

About 750,000,000 bases are read for sample against about 23,000,000 bases for controls, Q20 are equivalents. Alignment against references indicates that DNA is the same between samples and controls.

My questions are: do someone have experience using GenDx system with Proton? using GenDx barcode? Do mismatches in barcode reading are possible?

What about to play with basecaller--barcode parameters?

basecaller--barcode_filter 0.01 --barcode_filter_minreads 10 --phasing_residual_filter 2.0 --max_phasing_levels 2

Thanks a lot