Deciphering SAM formal Flag 0x0002

[sas]

Hello All,
In the SAM format specification 0x0002 corresponds to "the read is mapped in a proper pair". What constitutes a "proper pair"?
Thanks for your help,
sas

[nilshomer]

Hello All,
In the SAM format specification 0x0002 corresponds to "the read is mapped in a proper pair". What constitutes a "proper pair"?
Thanks for your help,
sas

Keep reading: "the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment)". So you should check out the behavior of the alignment algorithm.