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IndelRealigner and --downsample_to_coverage / -dcov
I ran the IndelRealigner tool with this option: --downsample_to_coverage 100000. i see this output line, which leads me to believe the downsample option was recognized:
INFO 09:42:26,159 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 100000
yet, i also see multiple lines like this in the output:
INFO 09:43:59,101 IndelRealigner - Not attempting realignment in interval gi|224589819:117115017-117313719:44370-44521 because there are too many reads.
i thought the downsampling would alleviate excluding regions where too many reads are present? i do believe the regions are being excluded because the IndelRealigner tool completes quickly, as compare to runs i've made when i've set the max to align to 100000.
to be explicit, i want all regions included in processing, and i'm willing to down sample to make this happen.
thanks for the help.