Open mincej opened 1 year ago
Sorry for the long delay, I'll try to help as I can. Maybe @vyepez88 can help too
the MappingQualityNotZeroReadFilter
does the following: Filter out reads with mapping quality equal to zero
So it shouldn't be associated with the read group (although I believe the current version of DROP should auto-detect a lack of read group and apply a dummy group).
Have you taken a look at your reads and look at column 5 (you can do this using samtools -h
Hi Joshua, is this still an issue?
Hello, I'm getting an error, which seems to be a result of all of my reads being filtered out in the BaseRecalibration step. Please see the info log below. I'm not too sure where to start with this issue, I'm more familiar with RNA-seq analysis and GATK is new to me. I previously had an error that was caused from no read group, so I added a general read group manually with AddOrReplaceReadGroups , so since everything is part of the same read group I'm guessing that something is failing and everything is being filtered out. Does anyone have any suggestions?