PCAWG - Duplications size

[Joan Frigola Rissech]

Good morning, I'm working with the structural variants data from PCAWG and I'd like to classify by size, mainly the duplications. I have a couple of questions:

1. How do I compute the size of the duplications? In most cases start and end coordinates are the same, and then there's an alt coordinate. What is this alt exacly? Is the size of the duplication the distance from start to alt?

chrstartendreferencealtgenealtGeneeffect

chr12725675627256756G]1:28028201]GNUDCintergenic regionDUP

2. I've observed that the column gene is never "intergenic region". Are these duplications filtered or restricted to coding genes?

Thanks a lot!

Joan

[Mary Goldman]

HI Joan,

I would recommend going to the PCAWG publications themselves to answer these questions. Their flagship paper is here: https://www.nature.com/articles/s41586-020-1969-6

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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