filtering properly paired reads and flagstat output

[volavii]

Hi,

i wanted to extract all reads out of my bam file, created with BWA2, having the flag: properly paired.
To do this, I used: samtools view -f P my.bam > my_propPaired.bam
To check if the filtering worked, I created also for my_propPaired.bam the samtools flagstat output with the expectation of getting 100% properly paired reads.
What I actually get was the identical flagstat output as for the original file (my.bam)

I compared the size of both bam-files and actually the my_propPaired.bam is smaller.

does anyone has an idea what happend here?

Many, many thanks in advance!!!

[dpryan]

Passing "P" to "-f" won't work, try "samtools view -o my_propPaired.bam -hbf 0x2 my.bam". I don't actually know if the "h" option is needed when you output to a bam, but you might throw it in there anyway (I'm assuming that you actually wanted a BAM file, since that's the extension you used in your example).

[volavii]

Thanks dpryan for the fast reply!

actually I used the -b option, just fogott to post it... :/ SORRY!!!!

i will try if it helps to change from P to 0x2 and using h.

[volavii]

solution found

it worked
so one should not use P! Using -f 0x2 resulted in 100% properly paired reads

[dpryan]

it worked
so one should not use P! Using -f 0x2 resulted in 100% properly paired reads

Never discount the power of hexadecimal!