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How does total number of reads calculated in UnifiedGenotyper
Dear GATK team,
From UnifiedGenotyper's output, there is a line indicating total number of reads that the tool works on. For example:
"INFO 01:11:47,861 TraversalEngine - 2710581 reads were filtered out during traversal out of 77522806 total (3.50%)"
Could you please explain how this number 77522806 get calculated? As I checked from our example, the input bam file contains 1,500,000 more reads than this. Apparently, some reads got filtered out from this total number. It would be great if you could advise on which filters have been applied to the input reads.
Thanks a lot for your time!