how to query rsid's using dbsnp in r or linux

Question

[Nance]

Hi,

I have a dataset of summary statistics however lots [millions...] of the snp names/rsid are missing and I want to add these. I want to add them using the chr / pos / a1 / a0 info that I have.

I know I need to use an existing database to do this - Much like how to query ensembl sql database - to check if a snp (name = rs...) is in an intron ? - however I do not have the snp name so this seems to hinder me? Most of the posts are designed for filling in snp info when you already have the name?

I downloaded the latest build from dbsnp https://ftp.ncbi.nih.gov/snp/latest_release/ however this is a whole database and I am finding it is too big to work with I think.

I also looked at the r package rsnps however you need the SNP names first - this has already been raised as a bug https://github.com/ropensci/rsnps/issues/122

Is there an easier way to do this? Can you use biomaRt to do it? I have seen this post Dbsnp : Best Way To Obtain Data On Snps and started running it however I do not have the SNP names

Thanks!

[cpad0112]

if you want to annotate your data with dbSNP, I would suggest to use tools such as bedtools, bcftools to annotate your data with dbSNP vcf.

[Nance]

Hi thankyou. However my other file [not dbsnp] is not a vcf so I can not use these tools [yet]. Do you know of a way I can convert this on the command line or otherwise? I keep seeing the use of:

mv file.txt file.vcf

or

cp file.txt file.vcf

As a conversion but this does not work for me! Thanks!

[cpad0112]

if you could post entries from text file, that would help understanding the issue.

[Nance]

The .txt file is very standard format:

Chr     Pos     rsID    A0      A1      Beta-A1 P            
chr1    11888   NA      T       C       -0.109  0.81     
chr1    11213   NA      T       C       0.215   0.46    
chr1    11234   NA      T       C       -0.135  0.8      
chr1    12567   NA      C       T       0.177   0.77   
chr1    13333   NA      G       A       -0.165  0.81

And the .vcf is from dbsnp latest release https://ftp.ncbi.nih.gov/snp/latest_release/VCF/

##fileformat=VCFv4.2
##fileDate=20210513
##source=dbSNP
##dbSNP_BUILD_ID=155
##reference=GRCh38.p13
##phasing=partial

And then more vcf lines until

#CHROM             POS     ID                       REF     ALT     
NC_000001.11    10001   rs1570391677    T           A,C       
NC_000001.11    10002   rs1570391692    A           C          
NC_000001.11    10003   rs1570391694    A           C     

So I would like to use columns chr / pos / ref allele / alt allele to 'fill in' or 'impute' the RSIDS in to the .txt file above. I have been told dbsnp is the best resource for this but really struggling to know how to combine these data.

Thanks!