Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Selecting homozygote calls using SelectVariants

sagipolanisagipolani Posts: 41Member

Hi,

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.

Thanks!

Sagi

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