Sheep reference genome remapping coordinates

Question

[valentinatsar]

Hi everyone,

The latest sheep genome assemblies (Ramb_v1.0, Ramb_v2.0) are not available at liftover (https://genome.ucsc.edu/cgi-bin/hgLiftOver) while the NCBI Remap tool has been unfortunately retired.

Do you have any ideas on how to convert sheep genome coordinates from older assemblies to the newest ones to proceed with functional annotation of specific genomic areas with Variant Effect Predictor?

Many thanks in advance, I would appreciate any possible solutions!

Answer 1

[Pierre Lindenbaum]

you can create your chain file using the recipe available here: http://genomewiki.ucsc.edu/index.php?title=LiftOver_Howto

Answer 2

[colindaven]

If you want to remap genes and have a gff3 file, then Liftoff would be a decent recommendation https://github.com/agshumate/Liftoff It is relatively simple to use.

Whether output will be good enough to use Ensembl VEP accurately remains to be seen. I guess your plan is to annotate SNPs ?

[valentinatsar]

Thank you for your response

As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequences. Yes, I need to annotate specific SNP markers.