Thank you for your help. I have a vcf file which is composed of 8 samples. I would like to us SelectVariants to get a vcf list of locations where sample1 is homologous alt or hetrozygous. I attempt to use vc.getGenotype("Sample1").isHet or variations around that but am having difficulty having the JEXL expression recognized. Any advice?
I think that you just need to enter the term for the search in the tool form box. For example:
isHet == 1
See item 4 here for the query structure rules: http://gatkforums.broadinstitute.org/gatk/discussion/1255/using-jexl-to-apply-hard-filters-or-select-variants-based-on-annotation-values
Please give this a try. Jen, Galaxy team