Variation graph mapping

[mattiassherman]

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

[jfy133]

Hi @mattiassherman !

I think it would be a great idea!

The only problem is that I don't know if any of the dev team any experience in variation graph tools (barring @aidaanva maybe?)

We would need someone with more expertise (you maybe?) who can help us check firstly it fits within the existing framework, and then implementing it. Also because none of the dev team really work on it currently, it maybe would not be highest priority (we need to get this major rewrite out first which is still a couple of months away)

Do you think you would be able to do that or know someone who could assist?

[mattiassherman]

Hi @jfy133 ,

I would happily contribute but unfortunately I don't think I quite have the expertise yet with either variation graph mapping or nextflow pipelines, although I will keep it in my mind for further along in my PhD! Perhaps once I have implemented vg as I described above, as I will have had more experience in both of those areas (and will hopefully be aware of any potential issues!).

Thank you for your response though! I really appreciate all the work the eager team puts in to standardise these pipelines!

Thanks,
Mattias

[jfy133]

OK, maybe then re-visit this issue in a couple of months once we've released eager v3, and you've progressed a bit further :)