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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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How to change BayesMaxPNorm (filter CNVs) without retuning the HMM step? #432

Open ranli2 opened 2 years ago

ranli2 commented 2 years ago

Thank you very much for this wonderful tool. It's part of my scientific life now.

I found there are some noises in the final CNV calling and I want filter some CNVs by changing (using lower) BayesMaxPNorm. I am wondering if the BayesMaxPNorm has been stored in the HMM process so I don't have to rerun the HMM procedure by setting a different BayesMaxPnorm? As I would like to try different BayesMaxPNorm for different dataset so rerunning the whole process would be time consuming.

Thank you very much in advance!

GeorgescuC commented 2 years ago

Hi @ranli2 ,

If you are using a the recent versions of infercnv and have not disabled the RDS backups at each step, you can simply rerun infercnv with the same data, settings, and output folder, but simply change the BayesMaxPNormal value and the reloading system should take care of it. The process will resume from step 19, which is to apply the cutoff to the already run Bayesian Network model. If you are running an older version of infercnv, you might have to rerun the Bayesian Network model as well as steps 18 and 19 used to be a single step. In either case, the HMM model should not be rerun unless you change one of the settings that affects any of the steps 1 to 17.

Regards, Christophe.