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Read Filter "Duplicates"

MaxMax Member
edited April 2014 in Ask the GATK team

Hi !

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 !

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  • MaxMax Member

    Hi Geraldine,

    thanks for your prompt answer !
    So then I would assume, the DuplicateReadFilter to remove the marked PCR Dups, the MappingQualityZeroFilter to remove Reads with MQ==0, the MappingQualityUnavailableFilter to remove Reads with a MQ that is not available and the NotPrimaryAlignmentFilter to remove reads that do not map uniquely (only the best (primary) one remains)

    Is that correct ?

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