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Selecting homozygote calls using SelectVariants

sagipolanisagipolani Posts: 41Member


Is there a way to select ONLY homozygote calls from a vcf file using SelectVariants?

I understand that the GT for homozygotes is 1/1, whereas the genotype for heterozygotes is 0/1. But when I ude the following command, I get an empty vcf file (i.e. only with a header):

$ java -Xmx4g -jar GenomeAnalysisTK.jar -SelectVariants -R reference.fasta --variant input.vcf -select 'GT == "1/1";' -o output.vcf

I'd appreciate your help on this matter.




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