Variation graph mapping

Hi,

I was wondering if there were any plans to implement any graph mapping options in the eager pipeline?

I am currently using eager with bwa aln to map fairly divergent non-human genomes but this suffers from reference bias. I know this can be partly mitigated with relaxed mapping parameters or by lowering mapping quality, but I would like to preserve a high mapping quality.

I am planning on using vg with a list of variants (as demonstrated in https://link.springer.com/article/10.1186/s13059-020-02160-7). In the absence of an implementation in eager, I will have to stop my eager pipeline prior to the mapping step and use the output fastq to run an adjacent script with vg, and use the BAM output to carry out the later steps of the eager pipeline.

Eager has been the standard pre-processing method in my lab for years but difficulties in changing pipeline versions has made changing key steps like these challenging to implement. I think adding this to eager would benefit a lot of people, especially those working on non-human organisms who don't always have good (or closely related) reference genomes.

I hope you'll consider this improvement!

Many thanks,
Mattias

Start by reviewing the eager mapping step and how it passes FASTQ input to mapping and BAM output to later pipeline stages. Compare the current bwa aln path with the requested vg workflow and determine the integration scope. Done means graph-based mapping can be selected in eager while preserving the downstream analysis steps.