I am somewhat new, but I feel that my problem should have a relatively straight forward answer. Other forum posts have covered similar but I wasn't able to resolve my issue. I have a vcf file with the analysis of 9 samples. I simply want to select sites based on a sample's genotype or subtract sites from a list based on observed genotypes (trying to identify a recessive disease causing mutation based on exon sequencing of affected, obligate carriers and unrelated controls. I am using GATK in windows command prompt if that matters.
java -jar GenomeAnalysisTK.jar -T SelectVariants -R ref.fasta -V input.vcf -o output.vcf -select 'vc.getGenotype("samplename").isHet()'
results in:
<h5>ERROR</h5> <h5>ERROR MESSAGE: Invalid JEXL expression detected for select-0 with message</h5>java.lang.String cannot be cast to java.lang.Boolean
<h5>ERROR</h5>I have tried countless variations on the commands, format and syntax but am unable to make progress. Any help would be appreciated. Thank you.
