Ensembl phylogenetic context

Question

[gokberk]

Hi, I was wondering if there is a way to download or generate 24 primates EPO-Extended alignments for a set of SNPs using Ensembl VEP. I can download it from the phylogenetic context section in Ensembl for a given SNP, but was wondering how to do it for a large number of SNPs from command line.

Thanks!

Answer 1

[Emily]

There isn't a method in the VEP or any of the VEP plugins that do this, so you would need to write something yourself. You could invoke the alignment REST API endpoint, to fetch the alignment ± whatever up/downstream distance you want.

[gokberk]

Got it, thank you!

[gokberk]

Hi again Emily_Ensembl , I have quick follow-up question. All my SNPs are annotated in GRCh37 coordinates. Is there a way to get GRCh37 sequence using the code you pointed to?

I've been using the code chunk below:

server <- "http://rest.ensembl.org"
ext <- paste0("/alignment/region/homo_sapiens/", tmp_chr, ":", tmp_seq_str, "-", 
              tmp_seq_end, "?species_set_group=primates")

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

I tried my chance with /alignment/region/homo_sapiens/GRCh37/, but didn't manage to make it work. I was wondering if there is a simple way or if I have to CrossMap all my SNPs.

Thanks!

[Emily]

server <- "http://grch37.rest.ensembl.org"

[gokberk]

Many thanks!!

[gokberk]

I have just tried this, but it doesn't seem to be working for GRCh37. I received the following error: "No method_link_specices_set found for method LASTZ_NET and species_set_group primates "

[Emily]

Ah, yes, I forgot. There's no comparative genomics data available on GRCh37. It got out of date so we removed it.

[gokberk]

Oh I see, I will lift over my SNPs to GRCh38 then, thanks a lot for all your help! :)