Tagged with #mappingqualityzerofilter
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Created 2012-07-23 23:56:09 | Updated 2012-07-23 23:56:09 | Tags: mappingqualityzerofilter gatkdocs
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A new tool has been released!

Check out the documentation at MappingQualityZeroFilter.

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Created 2015-03-12 12:18:55 | Updated | Tags: duplicatereadfilter mappingqualityzerofilter
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Hello GATK team,

BaseRecalibrator applies the filters: DuplicateReadFilter MappingQualityZeroFilter I've noticed that in the bam after PrintReads, most of those reads indeed filtered out, but few of them were left - about 2% reads that were marked as dups by picard, and 4% reads with a mapping quality zero.

What exactly happens when a tool applies a filter?