Issues with identifying chromosomes for a list of SNPs

Question

[ks.sholohova]

Hello everyone!

Today I was trying to check whether all SNPs in my list (thousands of SNPs, GRCh37) belong to the particular chromosome (let's say chr 19) but I had some issues with it. I am doing everything on R and my strategy was this:

1. To prepare list of SNP as a file (all starts with rs...)
2. To download the human chromosome 19 from dbSNP
3. To search my list as a pattern within downloaded chromosome

However, downloading process of chr 19 is going on for many hours already... And the fastest download option doesn't give the proper information for analysis.

I would love to know whether there is another way to check the list of SNPs for belonging to the particular chromosome in R?

Thanks in advance!

[rpolicastro]

Can you provide the code you are using for this and some example data?

[ks.sholohova]

I'm sorry that I did not reply to you! I am a bit new to bioinformatics and could not find a proper example data. However, @zx8754 helped me to resolve this question. May you have a nice day!

Answer 1

[zx8754]

Usign biomaRt:

#set up
library(biomaRt)
snpmart = useEnsembl(biomart = "snp", dataset="hsapiens_snp")
#Other useful functions
# listAttributes(snpmart)
# listFilters(snpmart)

Get SNPs that match with our list of IDs, here we have 2 SNP from chr1 and 1 SNPs from chr2:

getBM(attributes = c("refsnp_id", "chr_name", "chrom_start", "chrom_end"), 
      filters = c("snp_filter"), 
      values = list(c("rs17599629", "rs1218582", "rs11902236")),
      mart = snpmart)

#    refsnp_id chr_name chrom_start chrom_end
# 1 rs11902236        2     9977740   9977740
# 2  rs1218582        1   154861707 154861707
# 3 rs17599629        1   150685811 150685811

Now, to return only the ones which are on chr2, we can add "chr_name" filter:

getBM(attributes = c("refsnp_id", "chr_name", "chrom_start", "chrom_end"), 
      filters = c("chr_name", "snp_filter"), 
      values = list(c(2),
                    c("rs17599629", "rs1218582", "rs11902236")), 
      mart = snpmart)

#   refsnp_id chr_name chrom_start chrom_end
# 1 rs11902236        2     9977740   9977740

[ks.sholohova]

Thank you very much for such a nice explanation! May you have a nice day!