[Vcftools-help] Representation of large precise complex deletions

[Steven R. <sr...@fo...>]

Hi,

For “readability” we were looking at representing largish deletions (say > 1kb) in VCF using the symbolic key approach illustrated in the VCF docs for a simple deletion when treated as a structural variant – using a “<DEL>” symbolic key for example.

But I had two questions.  First, consider a “simple” deletion which I represent below two alternative ways.  Although this is a small deletion for illustration and we would use the first approach, we would consider the second approach for a much larger deletion.

#CHROM POS ID  REF   ALT    QUAL FILTER INFO
2      100  .  TACT  T      30   PASS   SVTYPE=DEL;END=103;SVLEN=-3
2      100  .  T     <DEL>  30   PASS   SVTYPE=DEL;END=103;SVLEN=-3


But what about a similar but “complex” deletion, where the ACT sequence is deleted but a G inserted.

#CHROM POS ID  REF   ALT    QUAL FILTER INFO
2      101  .  ACT  G      30   PASS   SVTYPE=DEL;END=103;SVLEN=-2

First, is SVLEN -2 (len(alt)-len(ref)) or -3 (end-pos+1)?   The docs would seem to suggest the former (-2), a net change in length rather than the number of reference bases involved, but wanted to confirm.

Second, how would you represent this using the symbolic key approach?  (Again, illustrating using this short variant, but it would only be of interest for a larger event.)

Using the approach illustrated for a simple deletion places the “<DEL>” string in the ALT field, meaning the ALT=G is unspecified.
#CHROM POS ID  REF   ALT    QUAL FILTER INFO
2      101  .  A  <DEL>      30   PASS   SVTYPE=DEL;END=103;SVLEN=-2

Alternatively, one could imagine putting “<DEL>” in the REF fields instead:

#CHROM POS ID  REF   ALT    QUAL FILTER INFO
2      101  .  <DEL>  G      30   PASS   SVTYPE=DEL;END=103;SVLEN=-2

This permits the alt alelle(s) to be specified, but the examples in the v4.3 spec never use a symbolic reference in the “REF” field.

Thanks.




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