SNPs file for reference genome (Mouse - GRCm39)

Question

[David Martínez]

Good morning to everyone. I write because we are trying to change from GRCm38 to GRCm39, and we need a new GTF file that contains all known SNPs for my project. I have the old one, but I need the new version (to run Reditools) and I can't download it from the Ensemble website.

Thank you very much in advance.

David.

[Ram]

Using all caps on online forums is bad etiquette. Please be mindful of that in the future, I've fixed your title this time.

[David Martínez]

Sorry, I'm not used to use online forums. I will try to read the rules next time. Thank you.

Answer 1

[vkkodali_ncbi]

You can use the NCBI Genome Remapping Service to remap the features annotated on GRCm38 to GRCm39. Choose the source and target assemblies as shown in the screenshot below:

we need a new GFT file that contains all known SNPs for my project.

I am not familiar with this format. If you mean GTF, then SNPs are typically not represented in this format. For gene and transcript annotation in GTF format, you can download the data on GRCm39 directly without having to remap. For SNP data, you will have to first download the data in VCF fromat from Ensembl EVA and then remap to GRCm39.

[David Martínez]

Thank you very much for your comments, I will try that. And yes, it was a mistake (I wanted to say GTF not GFT).

David.

[vkkodali_ncbi]

GTF file with gene/transcript annotation for GRCm39 assembly by NCBI RefSeq is here: https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/10090/109/