Previously, I had a list of variants as well as whole genome data from several individuals in .TPED and .TFAM format. I (with the guidance of biostars users!) used plink to find out which variants are in LD with the list of variants.
Now that I have a combined list - that is, the original list of variants and all of the variants in LD with those - how might one sort each variant based on (1) its activity in different cell lines and (2) its location in the genome/which gene it belongs to (ie, does the variant fall inside a promoter, enhancer, exonic gene region, etc).
The combined list is in .bed format (i can also get it in .tped format)
Also, from using plink, I could not get the combined list to categorize which variants are the LD bodies (and if so, which original list variant is it in LD with) and which are the original list variants - I'd like to categorize it by that as well.
Thanks!
