VCF liftover for mouse strains

Question

[TheWonderer]

Hi there, I'm working on an allele skew project where we are utilizing two mouse strains. In order to perform some QC, we would like to extract strain specific SNP info and we would like to know the SNP position based on the strain of interest, not the reference mm10. Therefore, we were thinking about performing a liftover to "convert" the coordinates. Anyways, I identified GATK LiftoverVCF as a possible tool but it requires a chain file that's seemingly not available. Would anyone have any suggestions for either making a strain specific chain file or a different tool that doesn't require a chain file? Thank you!

The specific question that we want to answer: How many uniquely mapped reads overlap with a SNP position of each strain?

[TheWonderer]

I'm going to try and use https://github.com/wurmlab/flo#using-flo as a method for creating the required chain file. Let me know if there are other suggestions.

Answer 1

[TheWonderer]

The method I decided to use is the Coordinate remapping tool available through NCBI. It's very powerful and removes the need for a chain file. I may still end up using flo but here's the those two links:

Coordinate Remapping: https://www.ncbi.nlm.nih.gov/genome/tools/remap

flo GitHub: https://github.com/wurmlab/flo#using-flo