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  • Best way to get 1.3m genome positions for rsIDS (EMMAX output)?

    Hello, it's my first post so please be gentle!

    I have EMMAX GWAS output - RSid beta p-value. I need to get the chromosome number and position for these data so that I can make Manhattan plots. Can anyone suggest the best way to do this? I've never used the Ensembl perl API, but I've seen some references to Bioconductor packages? I use R but not Bioconductor.

    I do have a Python script that matches up lines, so I could run it against some PLINk output that incls chrN, pos and RSids - but it took 2 days to run matching 500k SNPs, so 1.3m will be a LOT worse!

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