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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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MAPQ quality threshold #352

Closed AriadnaColmeneroCobo closed 10 months ago

AriadnaColmeneroCobo commented 10 months ago

Hello!

You mentioned that Delly now handles PE and SR discovery independently rather than as a sequential process. Given this, I have another question.

In some papers, variants were selected if they had a MAPQ=60, which, as I understand, refers to the PE quality. Consequently, would it be appropriate to establish a threshold based on either MAPQ=60 or SRMAPQ=60, given that these are processes which, as you informed me, are now independent?

Thank you in advance.

Originally posted by @tobiasrausch in https://github.com/dellytools/delly/issues/347#issuecomment-1680549757

tobiasrausch commented 10 months ago

Sure, that's fine.