Filter paired & mapped reads from SAM/BAM file

[pirates.genome]

Hi,
I have SAM/BAM files of paired end Illumina sequencing obtained by BWA.

I want to filter out all reads having "proper pair" and both the reads of pair aligned to references. How can I filter them?

Thanks in advance...

[dariober]

Hi- This should filter out all the reads where both mates are mapped and the mates face each other (---> <---). (Make sure it does what you want!).

samtools view -F 2 input.bam > output.sam

Best

Dario

[pirates.genome]

Thats what I was looking for!

Thank you Dario for the reply. I was looking for the same.