Obtain rsID GWAS variants (9M)

Question

[spolo]

Hi everyone,

I have GWAS summary statistics with genetic variants (9M) and I want to obtain the rs that correspond to each of them. I have already download the VCF file of the whole dbSNP database but I do not know how to continue. I have already read the previous answers but they did not solve my problem. So in case anyone can help me I would be thankful. I am working with this type of data:

CHR SNP BP A1
1 chr1:732994:G:A 732994 A
1 chr1:758443:G:C 758443 C
1 chr1:794707:T:C 794707 C

Answer 1

[bk11]

You can create the file using Chromosome, Position and SNP (rsid) from the VCF file of dbSNP database and merge that with your GWAS summary stats file.

head dSNP_database.txt
SNP RSID
chr10:10000000 rs1223870629
chr10:100000000 rs925217917
chr10:100000003 rs537453558
chr10:100000004 rs1382475200
chr10:100000005 rs530933119
chr10:10000001 rs369318156

head your_gwas_sumstats.txt
CHR SNP BP A1
1 chr1:732994:G:A 732994 A
1 chr1:758443:G:C 758443 C
1 chr1:794707:T:C 794707 C

awk -F '[: ]' '{print $1,$2":"$3, $4, $5, $6, $7}' test.file.txt |sed '1d' |sed "1i CHR SNP A2 A1 BP A1" >your_gwas_sumstats_to_merge.txt
head your_gwas_sumstats_to_merge.txt
CHR SNP A2 A1 BP A1
1 chr1:732994 G A 732994 A
1 chr1:758443 G C 758443 C
1 chr1:794707 T C 794707 C

You can use R to merge between common SNPs or get all the SNPs with and without RSID of sumstats as follows-

dbsnp <- read.table("dSNP_database.txt", h=T)
sumstats <- read.table("your_gwas_sumstats_to_merge.txt", h=T)
merged_data <- merge(sumstats, dbsnp, by="SNP", all.x=TRUE)
write.table(merged_data, file="your_gwas_sumstats_with_rsid.txt", sep="\t")