If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

SelectVariants כרםצ multi gVCF file

PolaPola IsraelMember


I run VQRS on multi gVCF file, I wanted to use SelectVariants to filter out 1 sample with the following fields: all homozygote regions (1.1) in this patient with the number of Allele Frequency (AF) in the other patients in the multi file.

I am having a problem with command, I run the following command line:

java -Xmx20g -jar GenomeAnalysisTK-3.3/GenomeAnalysisTK.jar -T SelectVariants -R ucsc.hg19.fasta --variant recalibrated_variants.vcf -select 'vc.getGenotype("child").(isHomVar==1)' -o child.vcf

Any suggestions how to get the output I need ?

Thank you for your help,

Best Answer


Sign In or Register to comment.