[ensembl-dev] VEP75 input

Eva Goncalves Serra egs at sanger.ac.uk
Mon Mar 2 15:23:40 GMT 2015


Hi,

I am trying to use vep75 (with cache) and had to re-format my input (which was not in vcf/or other compatible formats) to the ensembl input format. Thought I have done this successfully but I get an error in a specific insertion:

Original file entry:
8:133984814 c.6056-29 G>GTT

Formatted to ensembl format:
8 133984816 133984814 G/GTT +

Error I get:
WARNING: start > end+1 : (START=133984816, END=133984814) on line 19.

My code to reformat the input was this:

      my @split = split(/\t/); # splitting file by tabs
      my @al = split(':',$split[1]); # getting the chr:pos
      my @al2 = split('>',$split[3]); # getting the ref>alt

      if ((length $al2[0]==1) && (length $al2[1]==1)) {
        print "$al[0] $al[1] $al[1] $al2[0]/$al2[1] +\n";
      } elsif (length $al2[1] > length $al2[0]) {
            my $sub = (length $al2[1])-(length $al2[0]);
            my $new = $al[1]+$sub;
            print "$al[0] $new $al[1] $al2[0]/$al2[1] +\n";
      } elsif (length $al2[1] < length $al2[0]) {
             my $sub2 = (length $al2[0])-(length $al2[1]);
             my $new2 = $al[1]-$sub2;
             print "$al[0] $new2 $al[1] $al2[0]/$al2[1] +\n";
      }

Am I missing something?

Thanks a lot!

Eva
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