I'm wondering which tool or program is:
- Most updated; doesn't use a superseded algorithm
- Runs very quickly (ideally, under 30s per VCF file)
- Able to be automated in some way for a large number of VCFs
- I need to at least have these groups: Africans, East Asians, Europeans, and South Asians. More specific groups are fine.
- Able to be run locally, as I have a lot of data
I am not looking to visualize the data or graph a PCA. My goal is to get a percentage match, or any closeness measure, for each group for each VCF file (assuming one sample per file). All VCFs are generated from microarray data.
For example, Eurogenes k13 and MDLP World-22, especially with oracle, have sufficient results but are only available as a web app.
To clarify, I am asking if there exists any such local program that exists that is peer-reviewed or validated, fast, and automate-able.