I am writing a small script to write a VCF file from short multiple sequence alignments, and stumbled into an interesting corner case.

This is the way a deletion should be represented in VCF format (I assume version 4+):

NC_000016.9  2138199 rs1799758   GTGAG   G  .   .  RS=1799758;...

But what happens if the deletion is at the first position? Immagine the following two aligned sequences:


How should it be encoded in VCF format? According to this thread on SEQAnswers, it might be necessary to include the first position after the end of the deletion, like this:

chromosome  1  AG G  .  .  [...]

Is this a VCF 4+ correct way to encode such variants?


1 Answer 1


From the latest VCF specs (page 8):

  1. REF - reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of the first base in the String. For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field), unless the event occurs at position 1 on the contig in which case it must include the base after the event;

So I think you're right


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