No Biological Application

[DarioS]

Looking at the preprint and vignette, I can't see use of svaNUMT on any biological data. The vignette uses chr1_numt_pe_HS25.sv.vcf but it doesn't have any mention of what that file is. Is it simulated data or biological data? It would be interesting to see this applied to a large dataset, such as 1000 Genomes, and show how it answers some biological questions. For example, when using NuMTs, do people cluster by ancestry (e.g. EAS, CEU, AFR) like they typically do by SNPs?

[jackieduckie]

Thank you for the suggestion. The example data used in the vignette is simulated data of human genome chromosome 1 (hg19) with simulated NUMTs. We have done additional work on applying svaNUMT on human cell line samples, and the results will be updated in the manuscript soon.