Dear all I wonder if there is a tool that allows remapping SNPs from one assembly to another in one step?
The solutions that I identified to solve this problem are either work with model organisms like NCBI Genome Remapping Service or require a chain file like LiftOver that are available for human, thale cress, mouse etc.
I need to remap (liftover) SNPs from one plant assembly to another without chain file, the plant is also nonmodel let say rapeseed or tobacco. So basically I have vcf file 1 for assembly 1 and assembly 2 for which I need a vcf file №2* with polymorphisms from **vcf file 1 with changed coordinates according to assembly 2. And I guess the solution should work through the direct BLASTing of coordinates with corresponding surroundings of polymorphisms.
If you know such tools please suggest one.