Question: Are there tools for SNP remapping (liftover) for non-model organism or ones that do not require chain file?
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gravatar for rimgubaev
3 months ago by
rimgubaev190
Russia/Moscow/Skoltech
rimgubaev190 wrote:

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.

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