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In VCF 4.2, a structural variant (SV) can be described with the BND keyword in SVTYPE. For example, the following example is an insertion (from https://samtools.github.io/hts-specs/VCFv4.2.pdf):

#CHROM    POS ID REF ALT                      QUAL FILTER INFO
2 321682  bnd V  T   ]13 : 123456]AGTNNNNNCAT 6    PASS   SVTYPE=BND;MATEID=bnd U
13 123456 bnd U  C   CAGTNNNNNCA[2 : 321682[  6    PASS   SVTYPE=BND;MATEID=bnd V

The keyword can be used to describe any SV event.

I would like to work out how to find out if an event is an insertion, deletion, duplication, inversion, etc. The algorithm/program will tell me the example above is an insertion.

I'm not able to find a tool that can do the conversion for me.

PS: The program I'm using is GRIDSS. This program would only generate BND in the SVTYPE field. It's not strictly a bug (BND can be used for any SV arrangement), but it's annoying in analysis.

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  • $\begingroup$ how about 'just' using the INFO/SVTYPEattribute ? $\endgroup$
    – Pierre
    Jul 16, 2018 at 12:58
  • $\begingroup$ @Pierre SVTYPE is BND. $\endgroup$
    – SmallChess
    Jul 16, 2018 at 12:59
  • $\begingroup$ @Pierre Some SV programs such as GRIDSS only output BND to the SVTYPE. Otherwise, I would not be here asking. $\endgroup$
    – SmallChess
    Jul 16, 2018 at 12:59
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    $\begingroup$ @Pierre My above example took from the specification. $\endgroup$
    – SmallChess
    Jul 16, 2018 at 13:02
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    $\begingroup$ If it uses BND to indicate an insertion, then it is not following the VCF specs since the SVTYPE for insertions should be INS and BND should only be used for break ends. $\endgroup$
    – terdon ♦
    Jul 16, 2018 at 13:58

1 Answer 1

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GRIDSS's author had posted his own solution on Github. The code is:

simpleEventType <- function(gr) {
    return(ifelse(seqnames(gr) != seqnames(partner(gr)), "ITX", # inter-chromosomosal
           ifelse(gr$insLen >= abs(gr$svLen) * 0.7, "INS",
           ifelse(strand(gr) == strand(partner(gr)), "INV",
           ifelse(xor(start(gr) < start(partner(gr)), strand(gr) == "-"), "DEL", "DUP")))))
}
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  • $\begingroup$ Can you please elaborate on this answer? What's gr? Looks like R, which library should I use for this? $\endgroup$
    – Wouter De Coster
    Feb 27, 2019 at 15:46

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