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When we run BaseRecalibrator i.e. the first phase of BQSR, we get some information in logs at the end of the process saying the following thing:
INFO 02:09:56,512 BaseRecalibrator - Processed: 1059663038 reads
INFO 02:09:56,514 ProgressMeter - done 1.06e+09 5.4 d 7.3 m 100.0% 5.4 d 0.0 s
INFO 02:09:56,514 ProgressMeter - Total runtime 464091.25 secs, 7734.85 min, 128.91 hours
INFO 02:09:56,514 MicroScheduler - 25351 reads were filtered out during traversal out of 45356 total (55.89%)
INFO 02:09:56,514 MicroScheduler - -> 155 reads (0.34% of total) failing DuplicateReadFilter
INFO 02:09:56,515 MicroScheduler - -> 25196 reads (55.55% of total) failing MappingQualityZeroFilter
INFO 02:10:00,308 GATKRunReport - Uploaded run statistics report to AWS S3
What does this phase means "filtered out during traversal"? Does it has some specific significance?