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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Q: Work for long reads data? #196

Closed zhengzhenxian closed 2 years ago

zhengzhenxian commented 2 years ago

Hi, Thanks for your great work, I am interesting that is octopus possible to work in PacBio HiFi or ONT long reads sequencing data? Or any suggestions if wanna transfer to long reads data?

Thanks!

zhengzhenxian commented 2 years ago

Hi, To clarify more, I am only referring to using octopus for somatic variant calling using long reads data.

Thanks!

dancooke commented 2 years ago

Hi, long-reads are not officially supported yet. You can try the latest develop branch and the bundled PacBio CCS config.

zhengzhenxian commented 2 years ago

Thanks! I might have a try on the config setting.

jelber2 commented 2 years ago

Just a comment that at least at the moment, I had to comment out 

#max-region-to-assemble=1000
#max-assemble-region-overlap=500
and 
#disable-early-phase-detection=true

in https://github.com/luntergroup/octopus/blob/2f91f5ed307d8ee659641a8232a41da6767fd841/resources/configs/PacBioCCS.config

based on using octopus 2f91f5e with PacBio CCS reads