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Aberrant VQSLOD scores
I recently reanalyzed a large number (>10,000) of targeted exome sequencing bam files using GATK 188.8.131.52 following the gatk4-germline-snps-indels cromwell workflows (haplotypecaller-gvcf then joint-discovery). (The bam files were produced a couple of years ago using BWA 0.7.10, Picard 1.123 and GATK 3.2-2 in a pipeline that included trimming, alignment (bwa), indel realignment, fixing read mates, marking duplicates and base quality recalibration.)
In the results, I noticed many deletions that felt unexpected. Looking at the bam files for those deletions, I find no read that overlap the deletion (although there are clipped reads that stop at the called deletion point). Looking more closely at the INFO field, I noticed that they have aberrant VQSLOD scores (VQSLOD score > 2e12). There is quite a clear gap in score between the rest of the loci (vqslod < 40) and those that I call aberrant (vqslod > 2e12). All the loci with aberrant vsqlod scores are indels.
Is this a known bug? What could lead to this?
Many thanks for your help!