Anders Goncalves da Silva

Hello. Yes, we are aware of this bug now. Working towards fixing it. Thank you everyone.

@nthomson50 running snippy with different sets of samples with the same reference will very likely change the core, and therefore the number of SNPs (as you suggest). `ref.fa` is just...

Or a BioProject... Although, additional logic would be needed here...

@Emiller88 and @matthdsm thank you for the review. I'll work on it over the weekend.

@Emiller88 that is true. I am working on adding the extra tests for different formats. I am also trying to work upstream to allow for compressed output. While the tool...

@maesaar i would be a bit suspect of the assembly as suggested by @asl --- unsure it would be fit for purpose. as i mentioned in https://github.com/tseemann/shovill/issues/150 our experience suggests...

I can confirm this is an issue too. I have run into the same problem.

Looks like most of the development has shifted over to minimap2 and bwa-mem2. Checkout: https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa And: https://github.com/bwa-mem2/bwa-mem2

It only works on Mojave if I give it one thread. @tseemann is on to something!

@begleynk thank you for the answer. I appreciate the conundrum.