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  • Left-normalisation of variants using R

    I'm writing a mitochondrial haplotyping script in R, and one of the things I needed to do was left-normalisation of INDELs. Because of the way the variants were originally defined, I'm using the notation <ref><pos><alt> for variants (e.g. ACCCCCTCTA8280A to describe a 9bp deletion at location 8280). Here's my script:

    Code:
    ## left-normalise INDELs                                                                                                                 
    ## derived from pseudocode from http://genome.sph.umich.edu/wiki/Variant_Normalization                                                   
    leftNorm <- function(ref.seq, ref, pos = NULL, alt = NULL){
        if(any(grepl("[0-9]",ref))){
            leftNorm(ref.seq=ref.seq,
                     ref=sub("^(.*?)([0-9]+)(.*)$","\\1",ref),
                     pos=as.numeric(sub("^(.*?)([0-9]+)(.*)$","\\2",ref)),
                     alt=sub("^(.*?)([0-9]+)(.*)$","\\3",ref));
        } else {
            equalRights <- (substring(ref,nchar(ref)) == substring(alt,nchar(alt)));
            while(sum(equalRights) > 0){
                substring(ref,nchar(ref))[equalRights] <- "";
                substring(alt,nchar(alt))[equalRights] <- "";
                emptyAlleles <- ((nchar(ref) == 0) | (nchar(alt) == 0));
                pos[emptyAlleles] <- pos[emptyAlleles] - 1;
                ref[emptyAlleles] <- paste0(substring(as.character(ref.seq),pos[emptyAlleles],pos[emptyAlleles]),
                                            ref[emptyAlleles]);
                alt[emptyAlleles] <- paste0(substring(as.character(ref.seq),pos[emptyAlleles],pos[emptyAlleles]),
                                            alt[emptyAlleles]);
                equalRights <- (substring(ref,nchar(ref)) == substring(alt,nchar(alt)));
            }
            leftChangeable <- (substring(ref,1,1) == substring(alt,1,1)) & (nchar(ref) >= 2) & (nchar(alt) >= 2);
            while(sum(leftChangeable) > 0){
                substring(ref[leftChangeable],1,1) <- "";
                substring(alt[leftChangeable],1,1) <- "";
                pos[leftChangeable] <- pos[leftChangeable] + 1;
                leftChangeable <- (substring(ref,1,1) == substring(alt,1,1)) & (nchar(ref) >= 2) & (nchar(alt) >= 2);
            }
            paste0(ref,pos,alt);
        }
    }
    Here's a little test, using the example from here:

    Code:
    > all(leftNorm("GGGCACACACAGGG",c("CA8","CAC6C","GCACA3GCA","GGCA2GG","GCA3G")) == "GCA3G");
    [1] TRUE
    Note that the code uses vectorisable functions, so should work equally well on single values and vectors. A bit more tweaking is needed to get it to do the right thing on matrices.

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