custom gene set ?

[zhangpicb]

Dear @KangchengHou ,

Thanks for your great tool!

I have a question about make custom gene set. I read the custom gene set.

Step2 --snp-loc ${magma_dir}/g1000_eur.bim ,1kg SNPs are used.

But before I read the issue,I use the SNPs in the GWAS summary data to annotate gene,and then using the output file to Step3.

I follow (#2) to get gene set. And I find the these 2 output gene.out files are different.
Maybe Step2 --snp-loc should use SNPs in GWAS summary?

Thanks in advanced!

# Step 2: make gene annotation file for MAGMA using the following command, this only needs to be done
# once for different GWAS summary statistics, and the file will be saved to out/step1.genes.annot
mkdir -p out/step1
${magma_dir}/magma \
    --annotate window=10,10 \
    --snp-loc ${magma_dir}/g1000_eur.bim \
    --gene-loc ${magma_dir}/NCBI37.3.gene.loc \
    --out out/step1

[KangchengHou]

Yes you can use your .bim file. Just create .bim file that match with your GWAS summary.

[zhangpicb]

Thanks for your quick reply!