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Read Filter "Duplicates"
I just looked through the automatically applied Read Filters of the DepthOfCoverage Walker and saw that both, the NotPrimaryAlignmentFilter as well as the DuplicateReadFilter, are applied. However, according to the Docu, both should simply remove the marked PCR Duplicates.
I also realised that the MappingQualityUnavailableFilter and the MappingQualityZeroFilter seem to do the same things, too. (According to the documentation both filter out mapping quality zero reads. ).
Therefore I wondered, if there is a reason for these read filter "duplicates"; so is there any difference between the mentioned filters ?
Thanks for your help !