Answered on the GATK forum here:
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GATK filter on FORMAT FT tag added by Variant Filtration
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.
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