Explain the definition of DELLY output

Question

[maheetha.b]

I'm looking at a DELLY annotated file,

I am having some difficulty visualizing the difference between PairEndReadSupport, SplitReadSupport, TumorVariantCount, TumorSplitVariantCount, TumorReadCount.

Can someone familiar with DELLY output explain the differences between these? I assume that Paired End Support are basically how many total paired end reads support that structural variant. And I thought Split Read Support was how many split reads support a structural variant. But I thought that was supposed to be the Tumor Split Variant Count, and I don't how this relates to Tumor Variant Count.

[maheetha.b]

Thank you for the responses. This has been helpful.

Answer 1

[trausch]

There is an online Cancer Genomics Tutorial available for Delly that explains many of these INFO fields. There is also a separate Delly user group that has some info about this.

[nirvana]

cancer genomics tutorial link is not working. Please post the working link. Facing problem with understanding DELLY output especially in case of BND type (translation)

[trausch]

I updated the above link (I meanwhile extended the old Delly tutorial in a larger variant calling tutorial)

[shubhra.bhattacharya]

I have the same issue as indicated in the link below. Specially how co-ordinates are mapped during translocation events.

DELLY SNV detection output intrepetation

[shubhra.bhattacharya]

https://groups.google.com/forum/#!msg/delly-users/6Mq2juBraRY/Pj4NVGdvHAAJ

[cmdcolin]

The Cancer Genomics Tutorial book link is broken :{

[trausch]

Updated the link. The section about delly is "SV Calling"

[cmdcolin]

Thanks so much :) appreciated