How to filter multi mapped reads from human and chimp WGS data?

[s1rloin5teak]

my brother is running into a bit of a wall with a project. I'm trying to help him but I'm also not sure about this.

He's got some whole genome sequencing data and a big problem. he needs to filter out reads that map to both a human and a chimp reference genome.
He also needs to be able to identify and extract reads that map uniquely to just one of them.
He's got the resulting indexed BAM files, but isn't really sure which package, program, or tool is the best for this.

I know this is like a pretty common issue, but he's not finding a straightforward solution. Any ideas?

 

[TropicalMe]

Just filter BAMs with mapping quality and intersect/exclude against the other genome. Another option is BBMap or BamTools for more flexible filtering. It's a common comparative genomics workflow, just depends how strict he needs the said unique part to be