Given QTLs and genome annotation, quickly list genes closest to QTLs

Question

[michael.nagle]

I have GWAS data with many associated loci. I'm looking for a way of listing all of the closest genes (and their positions) without clicking through in a genome browser for every locus.

I wish to provide an input of the genome annotations (in .gff3 or another format) and a list of every associated loci (Chr and base position) and get an output of several of the closest genes and their start and stop positions.

I assume there's already some off-the-shelf package I can use for this, or at least some code.

Thanks for the help!

Answer 1

[pfs]

Have you looked into ANNOVAR?

[michael.nagle]

I'm looking into it now. I found instructions on their website for adding gene definition databases for non-human species, but they need to be in the USCS Genome Browser. I'm studying poplar, which is not... but I found in literature ANNOVAR was somehow used for rice, which isn't either.

Do you know how to add databases for species not included in the USCS Genome Browser, or could you point me in the right direction? Thanks.

[pfs]

I do not have first hand experience doing this but the 'Experimental Design' section in 'Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR' should get you started. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718734/