GATK filter on FORMAT FT tag added by Variant Filtration

[mimi_lupton]

I am trying to filter a VCF file that has been annotated by GATK variant filtration at the sample level.
For example in variant filteration if I used;
--genotypeFilterExpression "DP <= 4" --genotypeFilterName "DP4"

Now I want to change all the calls with this flag to missing.
I have tried to look at the GATK forum, but I'm afraid it is all going over my head!

I think I need to use SelectVariants, but make a JEXL expression???!!

I guess this is quite a normal thing to want to do. Any help would be greatly appreciated.

[vdauwera]

Answered on the GATK forum here:

http://gatkforums.broadinstitute.org/discussion/comment/8863/#Comment_8863