Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

Empty output when using VariantsToVCF with a simple BED file

kevyinkevyin Posts: 11Member
edited September 2013 in Ask the GATK team

java -Xmx2g -jar /share/ClusterShare/software/contrib/gi/gatk/2.6-4-g3e5ff60/GenomeAnalysisTK-2.6-4-g3e5ff60/GenomeAnalysisTK.jar -R /share/ClusterShare/biodata/contrib/gi/gatk-resource-bundle/2.3/hg19/ucsc.hg19.fasta -T VariantsToVCF -o bedtovcf.vcf --variant:BED single.bed --dbsnp /share/ClusterShare/biodata/contrib/gi/gatk-resource-bundle/2.3/hg19/dbsnp_137.hg19.vcf -L chr1


chr1 10153 10154 1

The output is empty

Post edited by kevyin on

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