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VariantFiltration of 1/1 only
I'm trying to use VariantFiltration to keep only SNPs with a 1/1 genotype
GenomeAnalysisTK -T VariantFiltration -R dm6.fa \
--variant H001.UniGenotyper.SNP.vcf \
--genotypeFilterExpression 'isHomVar==1' \
--genotypeFilterName "KeepHomVar" \
The GATK log states:
INFO 14:27:26,801 HelpFormatter - Program Args: -T VariantFiltration -R /mnt/lustre/scratch/bioenv/wg39/LHm_analysis/reference_sequences/dmel/v6.0/dm6.fa --variant H001.UniGenotyper.SNP.vcf --genotypeFilterExpression isHomVar==1
However, both heterozygous and homozygous-variant SNPs are still outputted to the resulting vcf file.
Could you help me correct this ? I'm guessing it's that the filter expression is not correct but I've tried a few alternatives to no avail.