SelectVariants JEXL expression not working as intended
I am trying to select all variants that are homozygous/polymorphic in either of two samples in my multisample vcf file. For example, Sample1 might be T/T (hom reference) while sample2 might be A/A (hom variant). To do so, I use the following code:
java -Xmx20g -jar $GATK -T SelectVariants -R $REF \ -V multisample.vcf \ -o out.vcf \ -select "'vc.getGenotype("sample1").isHomRef()' && 'vc.getGenotype("sample2").isHomVar()'"
However, the resulting out.vcf file still contains heterozygous calls for sample1 or sample2. I don't get any error messages, the tools just seems to ignore the command.
I am using version 3.6.
Any help insight would be appreciated.