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I have a tiny, 5000-line VCF file that I want to add dbSNP annotations to.
I'm surprised to see VariantAnnotator iterating along the millions of records in the dbSNP file, rather than the 5000 variants in the input VCF file. This will take 42mins on dbsnp 137...
Am I misunderstanding how this tool works, or just using it wrongly?
java -Xmx2g -jar /share/ClusterShare/software/contrib/gi/gatk/2.5/dist/GenomeAnalysisTK.jar -T VariantAnnotator -R /share/ClusterShare/biodata/contrib/gi/gatk-resource-bundle/2.5/hg19/ucsc.hg19.fasta --variant PG0000864-BLD_PGx_cleaned.vcf --dbsnp /share/ClusterShare/biodata/contrib/gi/gatk-resource-bundle/2.5/hg19/dbsnp_137.hg19.vcf --out PG0000864-BLD_PGx,GATK.vcf --validation_strictness SILENT