VCF output of speedseq(lumpy) SVtype BND are translocations?

[crazyhottommy]

Hi there,

Lumpy output vcf files with 4 different SV types: BND, DEL, INV and DUP, Something I have asked here

For BNDs:
I understand that if both break ends are in different chromosomes, this is more likely to be a translocation, but how about break ends on the same chromosome? I want to make sure that BNDs are always translocations or sometimes it is just SV types can not be determined and represented in the break end format.

I read here and saw DEL can be represented in BND format, but the example is showing break points on two different chromosomes, so it is a bit confusing.

Thanks for answering me.

Best,
Ming

[ernfrid]

In that example of a simple deletion the chromosome name is chr and the numbers are positions. Perhaps not the best choice, but it is intended to show BND entries on the same chromosome. Sorry for the confusion.

In terms of Lumpy output, I am not as confident as to the correct answer. I do think you are correct that if both breakends are on the same chromosome then the interpretation is that Lumpy was unable to determine that it belonged to any of the other classes (DEL, INV, DUP see https://github.com/arq5x/lumpy-sv/blob/7d60167d17347ceadb297e9a66c36df8013d1b83/src/lumpy/SV_VcfVariant.cpp#L110-L135). I would defer to @ryanlayer or @cc2qe on that though as I'm just guess from the source.

[cc2qe]

BND is a catch-all for a generic breakpoint, so you can't assume all to be translocations

When LUMPY reports a BND with both sides on the same chromsome, it is indicating misoriented reads (++ or --). When we see reciprocal evidence (both ++ and -- from the same event), LUMPY calls this an inversion. Howevere, when only one of these orientations are observed, it is designated a BND. Some of these "one-sided inversion" BNDs might be true inversions where we miss one of the sides, and others may be parts of complex variants or artifacts.

[crazyhottommy]

Thanks for clarifying this. So, a BND with both sides on the same chromosome can be an INV. Can it be a DUP or DEL?

[cc2qe]

LUMPY never represents breakpoints with DEL or DUP orientations as BNDs. Only one sided inversions and interchromosomal events

[crazyhottommy]

Great to know this!

Ming