How can I get chromosome number and position using SNP rs id?

Pawel Suwinski

Hi Mahantesh,

One way to search a large number of TSIDs is to run VEP:

http://asia.ensembl.org/Homo_sapiens/Tools/VEP

Another is to download the DBSNP database and use GREP or AWK to pick the annotations.

Pawel Suwinski

Hi Mahantesh,

The syntax below, you need to run either on UNIX or OS (Mac). The resulting file will be sorted by chromosomes and have the following fields:

#CHROM, POS, REF, ALT, QUAL, FILTER, INFO

=> Syntax for unzipped DBSNP file:

grep -w -f /path/to/your/list_of_rsids /path/to/dbsnp_file.vcf | sort -k1.4,1 -V -s > /path/to/your/new_file

=> Syntax for gzipped (GZ) DBSNP file:

zgrep -w -f /path/to/your/list_of_rsids /path/to/dbsnp_file.gz | sort -k1.4,1 -V -s > /path/to/your/new_file

Your RSID file should have 1 column. IF you have done the list in Windows, you need to convert to UNIX format (UTF8):

#nstall the package "dos2unix" in UNIX or OS:

sudo apt install dos2unix

#input the password

#then run

dos2unix -n /path/to/your/rsid_file /path/to/your/new_rsid_file

Hope it helps :-)