Contents
How many missing read group errors are there in Bam?
This table, generated by ValidateSamFile from a real BAM file, indicates that this file has a total of 1 MISSING_READ_GROUP error, 4 MISMATCH_MATE_ALIGNMENT_START errors, 894,289 MATES_ARE_SAME_END errors, and so on. Moreover, this output also indicates that there are 54 RECORD_MISSING_READ_GROUP warnings and 33 MISSING_TAG_NM warnings. 2.
Why is my GATK not working on BAM file?
You’re trying to run a GATK or Picard tool that operates on a SAM or BAM file, and getting some cryptic error that doesn’t clearly tell you what’s wrong.
How to diagnose errors in Sam or BAM files?
To fix these problems, you first have to know what’s wrong. Fortunately there’s a handy Picard tool that can test for (almost) all possible SAM/BAM format errors, called ValidateSamFile. We recommend the workflow included below for diagnosing problems with ValidateSamFile.
Why do I set mode = summary in Bam?
We set MODE=SUMMARY explicitly because by default the tool would just emit details about the 100 first problems it finds then quit. If you have some minor formatting issues that don’t really matter but affect every read record, you won’t get to see more important problems that occur later in the file.
What causes an invalid Sam or BAM file?
Invalid SAM/BAM files generally have one or more errors in the following sections: the header tags, the alignment fields, or the optional alignment tags. In addition, the SAM/BAM index file can be a source of errors as well.
Why are there SM tags in the BAM header?
If that happens to you, check whether your files have SM tags in the @RG lines in their BAM header. That is the most common culprit. However, if the command above outputs one or more of the 8 possible WARNING or 48 possible ERROR messages (see tables at the end of this document), you must proceed to the next step in the diagnostic workflow.