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.

VariantAnnotator on tiny VCF file

drmjcdrmjc Garvan Institute of Medical ResearchPosts: 4Member

Hi, 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?

thanks, Mark

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

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