Extracting unpaired reads from BAM file

[JChase]

Hello,

I'm a bit confused about the various SAM flags and how to selectively pull reads from a BAM file. I got a little carried away with samtools merge, and now I have a BAM file that includes paired as well as unpaired reads. Having both paired and unpaired reads in the same file is hindering some downstream analyses. I've figured out how to pull paired reads from the BAM file and put them into another BAM file, but does anyone know how I can pull unpaired reads from a BAM file and put them into a new BAM file? Or, alternatively, delete all paired reads from a BAM file, leaving only unpaired reads?

Thanks!

[swbarnes2]

Paired reads should have the 1 flag set. samtools view -F1 should get all the unpaired reads.

[JChase]

Paired reads should have the 1 flag set. samtools view -F1 should get all the unpaired reads.

Ah, thank you! I see now that my confusion was due to misunderstanding the -f vs -F options. I didn't realize different cases resulted in different types of filtering. Thanks again.

[lramsay]

Hello,

I'm a bit confused about the various SAM flags and how to selectively pull reads from a BAM file. I got a little carried away with samtools merge, and now I have a BAM file that includes paired as well as unpaired reads. Having both paired and unpaired reads in the same file is hindering some downstream analyses. I've figured out how to pull paired reads from the BAM file and put them into another BAM file, but does anyone know how I can pull unpaired reads from a BAM file and put them into a new BAM file? Or, alternatively, delete all paired reads from a BAM file, leaving only unpaired reads?

Thanks!

I am trying to pull paired reads from a BAM file. What options did you use to do that?

Thank you!

Edit: I was also confused about the upper vs. lower case options, but I think I get it now. Just to verify -f1 should get all the paired reads?

[nilshomer]

I am trying to pull paired reads from a BAM file. What options did you use to do that?

Thank you!

Edit: I was also confused about the upper vs. lower case options, but I think I get it now. Just to verify -f1 should get all the paired reads?

This site can help you get the flags correctly set: http://picard.sourceforge.net/explain-flags.html