How to extract properly paired alignments from a bam file using samtools?

Question

[pedrodcb]

This is what samtools flagstat returns :

87410692 + 0 in total (QC-passed reads + QC-failed reads)
17796957 + 0 secondary
0 + 0 supplimentary
0 + 0 duplicates
87410692 + 0 mapped (100.00%:-nan%)
69613735 + 0 paired in sequencing
34834040 + 0 read1
34779695 + 0 read2
19690094 + 0 properly paired (28.28%:-nan%)
65530882 + 0 with itself and mate mapped
4082853 + 0 singletons (5.87%:-nan%)
4317734 + 0 with mate mapped to a different chr
2061682 + 0 with mate mapped to a different chr (mapQ>=5)

Answer 1

[Ashutosh Pandey]

Hint: samtools view -f2

[pedrodcb]

Thank you for your answer Ashutosh, if it's not to much to ask would you care to explain me why? I am new to all of this, I have just started a bachelor in bioinformatics. Thank you!

[Ashutosh Pandey]

https://broadinstitute.github.io/picard/explain-flags.html

http://blog.nextgenetics.net/?e=18

[Kevin Blighe]

samtools view -f 0x02 also works