I'm having a plink file (ped map format) which I have subset for a list of SNPs and now I want to know with which genes these SNPs are related.
I did as the website suggested,
plink --file mydata --assoc
so the plink.assoc file was created as should be, but then when I run
plink --noweb --gene-report plink.assoc --gene-list glist-hg18
the plink.range.report file which should contain what I want, is empty.
I have manually checked and confirmed that for at least one SNP there is one corresponding gene.
When I run plink --noweb --gene-report plink.assoc --gene-list glist-hg18 --gene-report-empty
which is the opposite command, it contains all the genes of the glist-hg18 file.
At this point I am unable to think of a solution.