hurleyLi commented 6 years ago

Hi, could you please provide a script for converting BND svtype to specific SV types, e.g. DEL, DUP. I don't think the one in #4 is accurate. Thanks,

Danisov commented 2 years ago

I am also very interested. Did you find the solution?

walaj commented 2 years ago

Is this for germline or somatic rearrangement calling? If the latter, I would caution against converting to "DEL" "DUP" etc for reasons I can explain, and why I've never been excited about writing one (although others did which is fine). For germline, I haven't personally tested the script in

4 but it's essentially just doing a regexp to extract the four

possibilities from the BND annotation, so could use/fix that or make your own pretty easily.

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I am also very interested. Did you find the solution?

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walaj / svaba

Specific types of BND #28

4 but it's essentially just doing a regexp to extract the four