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maxReadsForRealignment value and depthofcoverage results don't jibe; indelrealigner
indelrealigner rejects a region because there are too many reads. --maxReadsForRealignment was set to 100000 for this run. when i run the depthofcoverage tool, it show that the max coverage in the region that was rejected is ~95000. many positions are far less, like around 1000. i don't understand why this region would be rejected since no position has a depth of coverage over the max i set with --maxReadsForRealignment.