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SelectVariants כרםצ multi gVCF file

PolaPola IsraelMember

Hi,

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,
Pola

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