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<div>Hi, </div>
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<div>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: </div>
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<div>Original file entry:</div>
<div>8:133984814<span class="Apple-tab-span" style="white-space:pre"> </span>c.6056-29<span class="Apple-tab-span" style="white-space:pre">
</span>G>GTT</div>
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<div>Formatted to ensembl format: </div>
<div>8 133984816 133984814 G/GTT +</div>
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<div>Error I get:</div>
<div>WARNING: start > end+1 : (START=133984816, END=133984814) on line 19.</div>
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<div>My code to reformat the input was this: </div>
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<div> my @split = split(/\t/); # splitting file by tabs</div>
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<div> my @al = split(':',$split[1]); # getting the chr:pos</div>
<div> my @al2 = split('>',$split[3]); # getting the ref>alt</div>
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<div> if ((length $al2[0]==1) && (length $al2[1]==1)) {</div>
<div> print "$al[0] $al[1] $al[1] $al2[0]/$al2[1] +\n";</div>
<div> } elsif (length $al2[1] > length $al2[0]) {</div>
<div> my $sub = (length $al2[1])-(length $al2[0]);</div>
<div> my $new = $al[1]+$sub;</div>
<div> print "$al[0] $new $al[1] $al2[0]/$al2[1] +\n";</div>
<div> } elsif (length $al2[1] < length $al2[0]) {</div>
<div> my $sub2 = (length $al2[0])-(length $al2[1]);</div>
<div> my $new2 = $al[1]-$sub2; </div>
<div> print "$al[0] $new2 $al[1] $al2[0]/$al2[1] +\n";</div>
<div> }</div>
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<div>Am I missing something?</div>
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<div>Thanks a lot!</div>
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<div>Eva</div>
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