How to check if a read in a Bam file is paired or not?

Question

[omariqbal2017]

From the flag bit 8, we can get obtain that the next segment in the template is unmapped so consequently, the read is not paired but this rule is not always true like in the case of flag value 129 so what's a reliable way to check if a read contains a pair or not?

[cschu181]

https://broadinstitute.github.io/picard/explain-flags.html Enjoy :P

"Mate unmapped" means the read is paired, just the mate doesn't map. What exactly do you want to know? Flag 1: read is paired (this is always set in paired-end data), flag 2: both map properly (i.e. FR orientation, same reference sequence; this is what you want in most(?) cases, but is useless if you want to link contigs for instance).