The IGSR has a [sample](http://www.internationalgenome.org/wiki/Analysis/Variant%20Call%20Format/VCF%20%28Variant%20Call%20Format%29%20version%204.0/encoding-structural-variants) 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  NA00001
1 2827693   . CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA  C . PASS  SVTYPE=DEL;END=2827680;BKPTID=Pindel_LCS_D1099159;HOMLEN=1;HOMSEQ=C;SVLEN=-66 GT:GQ 1/1:13.9

```

How 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?