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Explain the definition of DELLY output

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.

delly
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written by maheetha.b • maheetha.b

Thank you for the responses. This has been helpful.

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written by maheetha.b • maheetha.b

1 answer

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.

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written by trausch trausch

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)

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written by nirvana • nirvana

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

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written by trausch trausch

The Cancer Genomics Tutorial book link is broken :{

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written by cmdcolin cmdcolin

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

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written by trausch trausch

Thanks so much :) appreciated

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written by cmdcolin cmdcolin

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