percentBad parameter in VariantRecalibrator

flescai

Hi there,
I do apologise in case this question has been answered already but I couldn't find an updated thread on it.

In my previous code I had a conditional based on the number of samples to modify the percentBad parameter in VariantRecalibrator.
Now I get an error from my scala code as if the value were not anymore a member of the class.

Checking again in the Best Practices and in the VariantRecalibrator documentation I can't find it anymore.
Could you confirm it's not used anymore? or am I doing something wrong?

cheers,
Francesco

Geraldine_VdAuwera

Hi Francesco,

That argument has been deprecated in favor of -numBad; see the version release notes and technical docs for details.

Geraldine_VdAuwera

Hi Francesco,

That argument has been deprecated in favor of -numBad; see the version release notes and technical docs for details.