Help with finding whole list of known snps

Question

[angel0071987]

Hi there,

This is probably just a really basic/stupid question but...

I am looking for a list of all known equine SNPs for my WGS analysis pipeline. I have looked on ensembl under the variation section for the horse and I have downloaded the gvf file of all germline variations from the current Ensembl release for this species. But I have also looked on dbSNP and the newbatches section of that for the horse. I have downloaded the broad_genome batch that has 1163466 SNPs in, but then this isn't all of the known snps as other people have submitted new snps since.

Is the ensembl list the one that I want or am I missing something/doing it wrong.

Hope someone can help. Thanks in advance

Answer 1

[polarise]

The list of known SNPs for any organism will always be a work in progress because there are outstanding regions of the genome that remain to sequenced due to their complex nature (among other regions). Therefore, it makes more sense to start with what is available and keep the door open to re-running the analysis with a grown list of SNPs.

Answer 2

[EagleEye]

Hi angel0071987, you can find it here:

https://www.broadinstitute.org/ftp/distribution/horse_snp_release/v1/

https://www.broadinstitute.org/ftp/distribution/horse_snp_release/v2/

https://www.broadinstitute.org/mammals/horse