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.