How to intersect GWAS data with GTF or any other genomics annotation file?
Entering edit mode
3.0 years ago
jack ▴ 940


I'm new into GWAS, and I'm trying to intersect a GWAS data with GTF file. Here is the format of the GWAS data that I do have. I would like to intersect these data with GTF file. More specifically, I would like to figure out which SNPs sits where (gene, exon, intergenic, etc) in the genome. Is there any fast way of doing this?

                          SNP Freq.A1 CHR       BP A1 A2     OR       SE        P
4082040 rs3130820:29206683:T:A  0.9304   6 29206683  T  A 1.2806 0.017695 2.12e-44
4076284 rs3118360:28792030:G:A  0.9294   6 28792030  G  A 1.2823 0.017821 3.00e-44
1533336 rs1233578:28712247:A:G  0.8489   6 28712247  A  G 1.2228 0.014440 4.32e-44
7827373 rs9257566:29144532:C:T  0.9085   6 29144532  C  T 1.2684 0.017124 7.68e-44
genome gwas genetics SNP • 529 views

Login before adding your answer.

Traffic: 2320 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6