I converted bam files to fastq files to realign them with BWA. For some bam files, I get single end read files and files with incomplete pairs. I used the tool bam2fastq by biobambam2 which states single end reads as _s.fq.gz and incomplete pairs as _o1.fq.gz + _o2.fq.gz.
How do I align these files in the next steps? For some read groups i get all 3 outputs (also the "normal" output for complete read pairs which I usually use in the further analysis).