HaplotypeCaller advanced option --force-active missing

Hello.
From reading the docs for version 4.0.11.0 (and working with GATK version 4.0.12.0)

h ttps://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_haplotypecaller_HaplotypeCaller.php#--disable-optimizations

I see from the option --disable-optimizations documentation :
"Setting the --force-active and --dont-trim-active-regions flags may also be necessary."

However the option --force-active seems no longer available. Because I get this error message :

"A USER ERROR has occurred: force-active is not a recognized option"

Is this option no longer relevant and is the documentation out-of-date ? or should it still be present ?
(Older versions of the documetations also mention --force-active or -forceActive).

Thank you for clarification.

Answers

Sign In or Register to comment.