Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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