samtools view -f 4 inconsistency

[jpjp]

Hi,

I want to select unmapped reads in my bam file generated by bwa. When I use samtools view -f 4, it also selects some reads with flag 141 which does not contain 4. I can see that those reads are not mapped, but isn't -f 4 option supposed to pick up only those reads that have 4 bit set?

[jujubix]

4 in binary is 100, so '-f 4' will filter for any reads with the 3rd bit set to 1
141 in binary is 10001101, whose 3rd bit *is* set to 1, so seeing it is the expected behaviour

For more info on SAM flags, consider checking out these links and maybe a refresher on binary numerals.

[swbarnes2]

141=128+8+4+1

So yes, that read was unmapped. Specifically, it was the second read of its pair, it was unmapped, and its mate was unmapped too, and it is in the .bam file in its forward direction.

[jpjp]

jujubix and swbarnes2,

thanks for the explanation. It makes sense. For some reason I was doing the calculation in decimal.