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Error When Convert Human Snp138.Txt To .Vcf Format

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.

gatk
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updated by amin.sadvance • amin.sadvance • written by asphodel6 • asphodel6

1 answer

snp138 is already available as VCF: 

 curl -s "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz" | gunzip -c |  more
##fileformat=VCFv4.0
##fileDate=20130806
##source=dbSNP
##dbSNP_BUILD_ID=138
##reference=GRCh37.p10
##phasing=partial

you might just have to add a 'chr' prefix if you're using hg19.

• 428 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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