Reads traversed during IndelRealigner
Hi GATK team.
I am running GATK version 2.3. I've run a few jobs (with different reference sequences and Illumina read datasets) and noticed the same puzzling phenomenon.
When I run RealignerTargetCreator, I get the following output in the log...
96553 reads were filtered out during traversal out of 31487680 total (0.31%)
96137 reads (0.31% of total) failing MappingQualityZeroFilter
416 reads (0.00% of total) failing UnmappedReadFilter
Then, when I run IndelRealigner, I get the following puzzling output in the log...
0 reads were filtered out during traversal out of 20024 total (0.00%)
Previously, when I was using an earlier version of GATK (pre-2), the number of reads traversed during RealignerTargetCreator and IndelRealigner were about the same. Now, the IndelRealigner log always shows about 20000 reads traversed.
Should I be concerned about this?
Also...a quick question...will IndelRealigner still output a warning if the maxreadsforalignment threshold is exceeded for an interval (and therefore the region is returned as-is instead of realigned)?
Thank you for your help!