Finding if dbSNP type in biomart

Question

[zakkaknadine]

I have a list of dbSNP IDs for human chromosome 8 and I need to know which are SNPs and which are indels using biomart?

Is it possible to do so?

Answer 1

[finswimmer]

Hello,

it seems that this is not directly provided by biomart. What you can do is, select "Variant alleles" in the "Attributes" part. After you received the result, you can split this column by / and compare the number of characters to decide whether this is a SNP or INDEL.

fin swimmer

[zakkaknadine]

this worked, thank you!

[zx8754]

When comparing number of characters, also check if it has a dash: "-/C" is a SNP or an InDel?

Answer 2

[Mike Smith]

You can do this using the Ensembl REST API. Here's and example in R to get the info you're looking for:

library(httr)
library(jsonlite)
library(xml2)
library(dplyr)

## the rsIDs we're interested in
rs_ids <- c("rs1326880612", "rs1008829651")

## define the server and species we're querying
server <- "https://rest.ensembl.org"
ext <- "/variation/homo_sapiens"

## constructe the query based on the IDs we're using
query_body <- paste0('{ "ids" : ["', 
                     paste(rs_ids, collapse = '", "'),
                     '"] }')

## submit the query
r <- POST(paste(server, ext, sep = ""), 
          content_type("application/json"), 
          accept("application/json"), 
          body = query_body)
## check we got a valid respose from the server
stop_for_status(r)

## extract the vairant name and type
## reformat into a data.frame 
lapply(content(r), FUN = function(x) { 
        data_frame(name = x$name, var_class = x$var_class)
    } ) %>%
    bind_rows()

And the result...

# A tibble: 2 x 2
  name         var_class
  <chr>        <chr>    
1 rs1326880612 insertion
2 rs1008829651 SNP

Answer 3

[zx8754]

Using rsnps, interface for OpenSNP:

library(rsnps)

ncbi_snp_query(c("rs1326880612", "rs1008829651"))

#          Query Chromosome       Marker  Class    Gene Alleles Major Minor MAF    BP AncestralAllele
# 1 rs1326880612          1 rs1326880612 in-del DDX11L1     -/C  <NA>  <NA>  NA 10051            <NA>
# 2 rs1008829651          1 rs1008829651    snp DDX11L1     A,T     A     T  NA 10051            <NA>

[Mike Smith]

Nice, that's elegant.

[zx8754]

Thanks, yeah, if you wrap your code into a function, it would be elegant, too. That's what this package is doing anyway.