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empty vcf file after using VariantsToVCF

karin23karin23 Member
edited December 2013 in Ask the GATK team


i have SNPs from another SNP caller which does not produce vcf files so i wanted to convert those using the VariantsToVCF walker. I used the following command:

java -Xmx2g -jar  /PATH/TO/GenomeAnalysisTK.jar -T VariantsToVCF -R reference.fa -o mySNPs.vcf --variant mySNPs.bed

GATK version 2.7-4

i took a bed file as input which had the following format:

chr1    895 896
chr1    941 942
chr1    1096    1097

The walker runs without any error message but i get an empty vcf file (0B, nothing) apart from a mySNPs.vcf.idx and a mySNPs.bed.idx file.

Any idea how to fix that?

Thanks a lot!!!

Best wishes,

Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Karin,

    This probably indicates that the tool couldn't recognize the input format type. You may need to specify the format of your input variants file explicitly, e.g. if it's BED, you'd input it as --variant:BED mySNPs.bed.

  • karin23karin23 Member

    Hi Geraldine,

    thanks for the advive but, unfortunately, this does not help. I could also see before (when i didn't specify the file as a bed file), the following message: 'Dynamically determined type of mySNPs.bed to be BED, so it recognizes the file as a bed file.'

    Do you maybe have another idea?

    Thanks and sorry for bothering again,

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hmm, either something is wrong with the file's formatting or something's buggy in the conversion. I'm running a few tests locally to check if the tool is behaving properly, I'll let you know what I find.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Alright, it turns out the BED isn't actually a valid input for VariantsToVCF, even though it is listed as such in the docs. I'll try to sort out the inconsistency there, but in the meantime you'll need to generate your VCF some other way. Did your other SNP caller actually produce a BED file as output?

  • karin23karin23 Member

    Thanks Geraldine. No the SNP caller does not produce a BED file but a txt file with information on chr, pos, ref, alt, coverage ref, cov alt... and i converted it into bed because i thought VariantsToVCF works with bed.

    Bests, Karin

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah, no you may be better off trying to load that text file directly. That sounds like the old dbsnp format, possibly.

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