BLASR: How to subsample alignments from a region

Question

[shwethacm]

Hello!

I have an alignment of ~20x PacBio long reads to my reference genome and I am trying to extract alignments within only a certain region, say 2mb-10mb (sort of like samtools view ) but I am not sure how to do this.

I have alignments in the m4 format.

I think I should be specifying a region table but I am not sure.

Can anybody help?

[shwethacm]

Thanks, rhall.

I did eventually parse it myself but I was looking to check if I could be lazy about it and do it quickly using a preexisting tool :)

Well, now I know!

Thanks a ton anyway.

Shwetha

Answer 1

[rhall]

I'm not aware of any software to process m4 files, but they are straightforward to parse with simple scripts, https://github.com/PacificBiosciences/blasr/wiki/Blasr-Output-Format. If you are more comfortable with sam format, blasr can output sam instead of m4, the -sam parameter.