Tagged with #notprimaryalignmentfilter
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Created 2015-09-02 03:06:31 | Updated | Tags: baserecalibrator notprimaryalignmentfilter unmappedreadfilter
Comments (1)

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


Created 2015-03-03 16:20:02 | Updated 2015-03-03 16:21:10 | Tags: duplicatereadfilter notprimaryalignmentfilter
Comments (2)

I have a quick question. What is the difference between DuplicateReadFilter and NotPrimaryAlignmentFilter? The documentation for each of them is identical; i.e.

Filter out duplicate reads.

Created 2013-09-18 05:08:04 | Updated | Tags: depthofcoverage notprimaryalignmentfilter
Comments (3)

Can someone point me to documentation on how I can run DepthOfCoverage without the NotPrimaryAlignmentFilter?