VariantCalling / PseudoCalling Parallelization

[apeltzer]

Could be worth trying

splitBams -> genotype/pseudo-call/genotype likelihoods -> stitchVCFs together

[EisenRa]

The modern microbial genome mapping pipeline SNIPPY parallelizes variant calling by chunking the reference (lines 301). The variant caller it uses is FreeBayes.

[apeltzer]

Nice, that's exactly my plan for speeding this up in EAGER2, too :-)

[jfy133]

I will close this unless it is requested again. I think we in aDNA we rarely encounter high coverage mapping to very large genomes (like plants), so I think the benefits over just simple multi-threading of a given genotyper would be minimal in most cases.