Forum:All sam flags specifying first mate?

Question

[jyu429]

Is there a list of all sam flags specifying first mates in a pair?

Is there also a list of all sam flags specifying second mates in a pair?

Answer 1

[John]

Technically, there aren't flags for specifying anything in a pair, because 'is a pair' is not a flag. 'has multiple segments' however is, and since this almost always means pairs, you start by setting -f 1 to select only multi-read fragments.

To specify the first mate in a multiple-segment use the flag 64, which we add to our 1 above to give -f 65

There is no way to specify second mate in a pair, for the same reason that theres no way to specify a pair. Your options are "NOT the first read" which would be -F 65 or select for "the LAST read" which would be 128 which again we add to -f 1 to get -f 129

Personally I'd go with -f 129 because mistakes will be more obvious when -f 129 has a different number of reads than -f 65. This should (logically) never happen - but aligners be trippin' yo'

EDIT:

Sorry, in typical fashion as soon as I hit post I realised I haven't actually answered your question -_-;

I'm not going to post the 2048 different combination of flags, most of which mutually exclusive, here, but here's some python to print it out for you:

for x in xrange(0,4096):
  binary = format(x, '#014b')
  if binary[7] == '1': print eval(binary)

[jyu429]

Oh, I see. Thanks, John!

Answer 2

[jyu429]

I'm not sure I follow? Maybe I should have been more specific. The website has certain flags which will make "first in pair" checked, like flag 83. I just want the set of all flags that make the "first in pair" checked and separately the set of all flags that make the "second in pair" checked.

[John]

Ah, yeah, sorry, I realised this is what you wanted as soon as I made the first post. its 00:48am here, so I shouldn't really be posting stuff :P

I've pasted the code to solve this for first in pair. I'm sure you can figure out how to modify it for last in pair ;)