Variant calling algorithm

[funnell]

Hello!

I was wondering about X-Mapper's variant calling algorithm. I see you have a link to QuickVariants in the README, does X-Mapper just call QuickVariants to generate those calls? Or are there any differences?

Thank you!

[mathjeff]

Are you referring to the --out-mutations argument?

The logic (details in the README) is supposed to be the same as for QuickVariants. The code for those kinds of things (--out-mutations, --out-vcf, and --out-refs-map-count) was copied from Mapper to QuickVariants and we try to keep them in synch.

If you encounter any unexpected differences between the two anyway, then if you let us know about them, we can try to update one of the projects to make their results match.

Thanks!