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PLINK gene report problem
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2.8 years ago
Earendil • 20
Sweden

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.

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19 months ago
United States

Can you check whether the latest PLINK 1.90 build has the same problem? (Note that it does not support the undocumented --gene-report-empty flag.) (Edit: oops, this should not have been an answer, but hopefully it will lead to one in short order.)

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PLINK 1.90 worked just fine! Should I move into using it rather than v 1.07?

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