On Monday and Tuesday, November 12-13, the communications team will be out of the office for a U.S. federal holiday and a team event. We will be back in action on November 14th and apologize for any inconvenience this may cause. Thank you for using the forum.

GATK BaseRecalibrator

nilus1432nilus1432 SingaporeMember

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

Answers

Sign In or Register to comment.