Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?