Help Please! Stuck in .bed format and need to convert for Impute2
I started with PLINK data files, and changed the .map file over to the UCSC .bed format in order to do LiftOver. Now I have the output from that (in UCSC .bed format), and need to get it ready for Impute2, but cannot figure how to change it into Impute2's required input format.
At this point, I'd even take advice on how to get my UCSC .bed files back into PLINK format, as it seems like I could alternatively feed it into SHAPEIT and then into IMPUTE2.
I'm completely stuck and any help is greatly appreciated!!
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What is Impute2's required format?
"The first 5 entries of each line should be the SNP ID, RS ID of the SNP, base-pair position of the SNP, the allele coded A and the allele coded B."
http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html
Can you paste a sample of what you've got at your disposal (data), and the exact format in which you would like it to be? Then, one of us will convert it using a script, possibly one-liner.
We're visual animals and work better with data in structures (rows and columns). Reading textual explanations costs us brain energy because language does not come naturally and is a learned ability.
Thanks!