Can anyone help me download the dbSNP data for Bos taurus ARS-UCD1.3?

Question

[K]

I downloaded the version from Ensembl, but the INFO field shows that dbSNP_150 has been remapped to ARS-UCD1.2, so the SNP IDs aren't being annotated when I use it. Is there another database where I can download the dbSNP data for ARS-UCD1.3? I've searched NCBI, but it's not there, and in the ENA database, I can only find the FASTA file.

Answer 1

[Arup Ghosh]

https://ftp.ensembl.org/pub/release-113/variation/gvf/bos_taurus/

Source: https://www.ensembl.org/Bos_taurus/Info/Index

[K]

thank you, do you have any scripts/commands for converting it to vcf files? i used "gffread input.gvf -T -o output.vcf" but i cannot sort the converted vcf file in bcftools due to undefined header.

[Arup Ghosh]

Check the following threads.

Generate GVF file from VCF file

Convert GVF to VCF