Testing Benchmarks

Explanation of Metrics

The coverage table is produced using BWA-MEM aligned BAMs on the GRCh38 reference genome. The BAMs are processed by GATK's CallableLoci tool with default settings. For a location to be considered callable it must have four reads overlapping the site. No more than ten percent of those reads may have a PHRED-scaled alignment quality of less than 10. Yielding a heuristic combined quality indicating less than 0.01% chance all the reads are aligned incorrectly to the site.

Callable - The total number of sites sequenced with 4 or more reads. Each read has less than 10% likelihood of being misaligned.

Total Loci - The sites having at least one read assigned. This metric is less useful when looking at a sample in isolation, but can be useful when looking at the population as a whole. The PAR regions are not included in these statistics as they are treated as part of the X chromosome due to recombination.