How to calculate minReadsAtLocus

Hello,
I would like to use the minReadsAtLocus from RealignerTargetCreator to select loci with high number of reads. For that I would like to first evaluate the "ReadsAtLocus" across the whole genome for my dataset.

The reason is that in my dataset, some regions (loci) have been heavily enriched and I would like to apply a sensible threshold after visual exploration.

Should I for example use DepthOfCoverage for this purpose? How should I adjust the parameters to get the same metric than the one used for minReadsAtLocus?

Answers

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