reorganise coordinates in a VCF using an agp

Question

[evoecogen]

Hello, A collaborator sent me a VCF generated by mapping 100 individuals to a reference genome. Let's call it scaffolded_reference. I discovered that there is a better genome of the same species out there, let's call it chromosomal_reference (the advantage is that I can identify sex-linked regions with it). I aligned the two genomes to each other and generated an agp with RagTag. The question is: is there a tool that I can use to reorganise my scaffolded_reference VCF using the agp? Thats is, change the chromosome annotations and coordinates to correspond to the chromosomal_reference, so that I actually know what chromosomes the SNPs are on? (An obvious alternative is to re-map to the better reference, but that will not happen now.)

Answer 1

[Pierre Lindenbaum]

is there a tool that I can use to reorganise my scaffolded_reference VCF using the agp?

https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard- but you'll need a chain file.

[evoecogen]

Thanks! A good solution. I have not done it yet, but there seem to be several agp to chain scripts floating around, so it should be easy.