Hi,

I ran a PLINK analysis using a large VCF file (with WES data), but since the VCF file wasn't annotated, I don't see any SNP IDs in my output. See the first lines below of my .bim file:

1   .   0   13221   T   G
1   .   0   13273   C   G
1   .   0   13281   G   C
1   .   0   13284   A   G
1   .   0   13289   C   CCT
1   .   0   13337   G   A
1   .   0   13350   A   G
1   .   0   13379   ACTC    A
1   .   0   13380   G   C
1   .   0   13395   C   T

My question is now whether there's a straightforward way to annotate the PLINK output (.e.g in R) instead of annotating the VCF prior to conversion (I saw this post Update 'ID' column in VCF file using BCFtools annotate about annotating the VCF file which I am trying to understand the ins and outs of). Or is there any other way I can retrieve the dbSNP information?

Many thanks for your help.