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I have used the following command $ java -jar GenomeAnalysisTK.jar -T VariantsToVCF -V:OLDDBSNP snp138.txt -R genome.fa -o snp138.vcf
to convert human snp138.txt file downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ to .vcf format.
As output the snp138.vcf file has been generated which has the size as 0 and the other 2 files have been generated as snp138.txt.idx and snp138.vcf.idx. How can i get the snp138.vcf?