A Brief Guide to Complex SV Orientations – a cartoon by Sage Wright – July 23, 2018

I don’t know about you, but sometimes in VCF files when I run into complex breakends and translocations, the formatting can get a little confusing. I made this handy cheatsheet that should hopefully help explain what’s going on should you come across these interesting structural variations.

Breakpoint Orientation Guide

Let me explain the table on the left side of this picture.. ±25 indicates the direction you should traverse the genome in order to gain sequence information about that particular region.

For example, if my VCF file said (This is taken directly from the VCFv4.3 documentation):

#CHROM POS ID REF ALT QUAL FILTER INFO

2 321681 bnd_W G G]17:198982] 6 PASS SVTYPE=BND

We would know that this is a +- orientation from the table shown in the picture above. If we wanted to get the 100 bp before the breakpoint on chr2, we would need to start from chr2:321681 and SUBTRACT 100 base pairs–so we would need the range of chr2:321681-321581.

If it were a -+ orientation, we would need to ADD 100 to the starting position. If this is confusing, consider this if we use the terms of  chrA and chrB. According to our VCF file, we are moving from chromosome 2 to chromosome 17. As shown beneath the table, the from chromosome is chrA, and the to chromosome is chrB.

If you have anymore questions regarding this concept, please let me know and I can try my best to answer your question. Or, if I’ve accidentally made an error in this chart, please let me know so I can fix it!

The VCF file format specification is another great resource if you want to try and understand this a bit better. However, it is heavy with jargon, which is why I tried to create this alternative. Regardless, I recommend reading it as it offers an additional reinforcement of these ideas in a way that might make more sense to you than my silly drawings. Cheers!