Why do some recommend using just the
-f 4 flag to get unmapped reads from a SAM/BAM file, while others have more elaborate extraction methods such as using a combination of
-f 4 -F 264, with
-f 8 -F 260, and
-f 12 -F 256. What is the difference between just using
-f 4 versus three separate steps? Also, why would one want to extract a mapped read with an unmapped pair, if the goal is to use just unmapped reads?
I haven't found a clear explanation for the differences but overall it does seem that majority use just the
-f 4 flag alone. But is this best practise?