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How to select samples that are polymorphic on a specific locus from a joint genotyped vcf file?
Hi, I am trying to select the samples that are polymorphic on a specific locus from a joint genotyped vcf file using SelectVariants tool and JEXL expressions with no success. The command I am trying to use is:
gatk SelectVariants \ --reference "/home/hg19.fa" \ --variant "/home/recalibrated_snps_recalibrated_indels_VQSR.vcf" \ --select 'POS == '11240190'' \ --select 'vc.getGenotype().isHet()' \ --output "/home/isHet.vcf"
Selecting on the position alone seems to work fine, but I want only the samples that are Het for this exact position, any suggestions please?
Thanks in advance