Question: Why are MI tags missing from some BAM entries?
Answer: The MI tag could be missing for a number of reasons:
- Not all reads will have a valid error-corrected 10x barcode. Those reads will not have an MI tag.
- Not all reads will be part of a molecule. For example, you may find some singleton reads that also have low mapping quality. Those reads will not be part of a molecule (and will not get an MI tag).
- For exome, you need at least one read that is on-target (maps to regions in your BED file) to get an MI tag. Most off-target reads will not get an MI tag.
For more information on the MI tag please see the Barcoded BAM documentation.