error when convert human snp138.txt to .vcf format

bulashabulasha GermanyPosts: 6Member

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?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,364Administrator, GATK Developer admin

    Let's try to find out why the conversion didn't work. Can you please post the console output that was generated when you ran the command?

    Geraldine Van der Auwera, PhD

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