Hi everybody, I downloaded the variants from 1000 Genomes project phase 3 (e.g ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr14.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz)
When I check structural variants with type = 'DEL' (VT=SV, SVTYPE=DEL), I see mostly reference with one base and alternative as <cn0>. I expect SV would have a much larger size, otherwise, they would be considered as INDELs. (most INDELs in the data are a few bases)
I am new to SVs. Could anyone give some insights ?