The IGSR has a sample for encoding structural variants in the VCF 4.0 format.An example from the site (the first record):#CHROM  POS   ID  REF ALT   QUAL  FILTER  INFO  FORMAT  NA000011 2827693   . CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA  C . PASS  SVTYPE=DEL;END=2827680;BKPTID=Pindel_LCS_D1099159;HOMLEN=1;HOMSEQ=C;SVLEN=-66 GT:GQ 1/1:13.9How to read it? From what I can see:This is a deletion (SVTYPE=DEL)The end position of the variant comes before the starting position (reverse strand?)The reference starts from 2827693 to 2827680 (13 bases on the reverse strand)The difference between reference and alternative is 66 bases (SVLEN=-66)This doesn't sound right to me. For instance, I don't see where exactly the deletion starts. The SVLEN field says 66 bases deleted, but where? 2827693 to 2827680 only has 13 bases between.Q: How to read the deletion correctly from this structural VCF record? Where is the missing 66-13=53 bases?
How to read structural variant VCF?
vcf;variants;structural
I just received a reply from 1000Genomes regarding this. I'll post it in its entirety below:Looking at the example you mention, I find it difficult to come up with an  interpretation of the information whereby the stated end seems to be correct,  so believe that this may indeed be an error.Since the v4.0 was created, however, new versions of VCF have been introduced,  improving and correcting the specification. The current version is v4.3  (http://samtools.github.io/hts-specs/). I believe the first record shown on  page 11 provides an accurate example of this type of deletion.I will update the web page to include this information.So we can take this as official confirmation that we were all correct in suspecting the example was just wrong.