BWA MEM mapping to divergent reference

[ellenell]

Hi,
I would like to use BWA MEM to map reads from a species without a reference genome to the closest available reference (about 3-4% diverged). What parameters could be changed to help allow for better mapping of more divergent reads?

[dkainer]

Hi Ellenell

did you ever figure out a good parameter set for BWA MEM (or any other aligner) for mapping with 3-4% divergence? I have a similar issue right now.

[Brian Bushnell]

BBMap, at its default settings, is very good for cross-species mapping; it tolerates down to a bit under 80% identity at defaults. You can increase the sensitivity by adjusting the parameters, but you shouldn't need to in this case.

[dkainer]

BBMap, at its default settings, is very good for cross-species mapping; it tolerates down to a bit under 80% identity at defaults. You can increase the sensitivity by adjusting the parameters, but you shouldn't need to in this case.

Hi Brian

thanks for the response. I have the BBmap suite (very comprehensive by the way!). I merged overlapping pairs using BBmerge, so about 45% of my read pairs are now single end. Is it a good idea to map the paired ends and then the single ends into two different BAMs and then merge into one BAM? or can BBmap handle both sets of inputs in one go?

cheers
david

[Brian Bushnell]

BBMap itself can only run single-ended or paired-ended in a single run, but it has a wrapper that can accomplish it, like this:

bbwrap.sh in1=read1.fq,singletons.fq in2=read2.fq,null out=mapped.sam append

This will write all the reads to the same output file but only print the headers once. I have not tried that for bam output, only sam output; I don't know if it would work with bam output.

[ellenell]

Hi,
No, I never did - we found it to work well enough under default parameters (only slightly lower % reads mapped for the divergent species than the reference species), and bwa-mem performed better than bwa aln alone, and similarly to a pipleline of bwa aln + stampy.