Extract mapped SE and properly paired PE reads from a bam file

Question

[Jautis]

Hello, I have paired end (PE) sequencing data performed on primarily small fragments of DNA. During the trimming/filtering process, we merged overlapping reads such that the resulting bam file contains a mix of now single-end and PE reads. I'd like to filter the mapped output for properly mapped read pairs or mapped single reads, can anybody help me figure out how to do that rather than just extract all mapped reads?

Thanks!

[jv]

one option is to use samtools view to pull out alignments with different alignment flags.

For more info on alignment flags see https://broadinstitute.github.io/picard/explain-flags.html