Hi everyone, We’ve been using sarek with iGenomes GATK hg38 references. We noticed, that for some genes e.g. PRODH, most reads also map to a highly homologous alternative chromosome location and thereby get a mapping quality of 0, which can be problematic especially for CNV calling. We use bwa-mem2 as aligner. This seems to be a known issue and masked reference genomes are recommended. However, I couldn’t find an official masked hg38 reference genome, only one from UCSC from 2014. Dragen uses a separate masking bed file. My workaround was to download the pangenome references from Dragen and mask the iGenome GATK fasta file with these regions, so replacing the nucleotide with “N”. This did resolve the issue and I get high quality alignments for this particular gene. We are a bit hesitant, if this is the correct way to do it, as we are modifying the GATK resource bundle. Are any of you using sarek and bwa-mem2 with a masked reference genome? If yes, what are you using? Thank you all in advance.