It is possible for a BAM to have multiple types of mate-unmapped records. These mate unmapped records are distinct from mate missing records, where the mate is altogether absent from the BAM. Of the three types of mate unmapped records listed below, we describe only the first two in this dictionary entry.
A mapped read's unmapped mate is marked in their SAM record in an unexpected manner that allow the pair to sort together. If you look at these unmapped reads, the alignment columns 3 and 4 indicate they align, in fact identically to the mapped mate. However, what is distinct is the asterisk
* in the CIGAR field (column 6) that indicates the record is unmapped. This allows us to (i) identify the unmapped read as having passed through the aligner, and (ii) keep the pairs together in file manipulations that use either coordinate or queryname sorted BAMs. For example, when a genomic interval of reads are taken to create a new BAM, the pair remain together. For file manipulations dependent on such sorting, we can deduce that these mate unmapped records are immune to becoming missing mates.
The second type of mate unmapped records apply to multimapping read sets processed through MergeBamAlignment such as in Tutorial#6483. Besides reassigning primary and secondary flags within multimapping sets according to a user specified strategy, MergeBamAlignment marks secondary records with the mate unmapped flag. Specifically, after BWA-MEM alignment, records in multimapping sets are all each mate-mapped. After going through MergeBamAlignment, the secondary records become mate-unmapped. The primary alignments remain mate-mapped. This effectively minimizes the association between secondary records from their previous mate.
GATK tools typically ignore secondary/supplementary records from consideration. However, tools will process the mapped read in a singly mapping pair. For example, MarkDuplicates skips secondary records from consideration but marks duplicate singly mapping reads.