Hi there, I am trying to filter BAM file with their 'flag' column. I am a little confuse about the meanings of, for example,
samtools view -f 4 -F 264 .....
I check the documentation, and notice
-f means 'what I want' and '4' means 'read unmapped' -F means 'wipe off' and '264' means 'mate unmapped + not primary alignment'
My question is:
If a sequence's flag is 12, will it be extracted by '-f 4'? If a sequence's flag is 8, will it be wiped off by '-F 264'?
I am confuse about the mechanism of this code, which is unfortunately not clear in the documentation.
See SAM Format site for explanation of the flags.
Also see Bitwise Flag Explained