Get Rs Number Based On Chromosome and Position in GWAS summary statistics

[Mayra Aldecoa]

Hello! I'm trying to munge the GWAS files but I have the SNP notation in "Chr:position_variant" and I don't know how to convert it in the "rs" notation requested. I've been diving in the web but apparently all the tool I found use VCF files. Do you have any suggestions to me to make this task?

Kinds!

[Jeff Kim]

Hi Marya Aldecoa,

This is a bit of a crude way to do it, but I often just read another tsv file with rsID and SNP data and merge with the GWAS summary statistic.

Following are variants from 1000 Genomes, processed by developers of GWASLab:

hg19: https://www.dropbox.com/s/37p2u1xwmux4gwo/1kg_dbsnp151_hg19_auto.txt.gz?dl=1

hg38: https://www.dropbox.com/s/ouf60n7gdz6cm0g/1kg_dbsnp151_hg38_auto.txt.gz?dl=1

This should cover 99% of the variants, including the HapMap 3 variants for LDSC.

Regards,

Jeff

[Mayra Aldecoa]

Thanks so much!