long reads default mapq lowered to 1: help text for dysgu call still says pacbio and nanopore mode has --mq 20

kcleal / dysgu

Toolkit for calling structural variants using short or long reads

MIT License

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long reads default mapq lowered to 1: help text for dysgu call still says pacbio and nanopore mode has --mq 20 #70

Closed tbenavi1 closed 9 months ago

tbenavi1 commented 9 months ago

Hello,

In version 1.6.0 I believe the default mapq for long reads was lowered to 1. However, the help text for dysgu call incorrectly says that --mq is set to 20.

Also, I was wondering for the reason for the change? Does this change improve sensitivity without getting too many false positives? Do you have a recommended value for mq? Thanks for any information.

kcleal commented 9 months ago

Hi @tbenavi1, Thanks for pointing this out, I will get it changed. Changing to mq 1 resulted in a small improvement in sensitivity and precision, especially for the CMRG benchmark. I think this is because including lower mapq reads results in a better quantification of the evidence