Tagged with #unmappedreadfilter
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Created 2015-09-02 03:06:31 | Updated | Tags: baserecalibrator notprimaryalignmentfilter unmappedreadfilter
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After running BaseRecalibrator we got : INFO 12:01:19,574 TraversalEngine - 1493749 reads were filtered out during traversal out of 5418149 total (27.57%) INFO 12:01:19,574 TraversalEngine - -> 824329 reads (15.21% of total) failing NotPrimaryAlignmentReadFilter INFO 12:01:19,574 TraversalEngine - -> 558510 reads (10.31% of total) failing UnmappedReadFilter INFO 12:01:19,574 TraversalEngine - -> 110910 reads (2.05% of total) failing ZeroMappingQualityReadFilter

What does the NotPrimaryAlignmentReadFilter, UnmappedReadFilter means?

I could figure out that mapping quality zero which means they're mapped but with zero confidence, so are useless.

Does it implies that there is problem in alignment?

thanks