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SelectVariants - Error

tinutinu Member Posts: 48
edited November 2013 in Ask the GATK team


I am trying to subset a few samples from a VCF using the following command

java -Xmx8g -jar GenomeAnalysisTK-2.6-4-g3e5ff60/GenomeAnalysisTK.jar -T SelectVariants -R Homo_sapiens_assembly19.fasta -V Input.vcf -sf samples.txt-o Out.vcf

Getting the error

ERROR MESSAGE: Key Indel_FS,Indel_QD found in VariantContext field FILTER at 1:985458 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.

I checked the Input.vcf and can find that the following lines exists in the VCF


Not sure why the error ?

Any help much appreciated..
Many Thanks,

Post edited by Geraldine_VdAuwera on

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,677 admin

    Hi Tinu,

    For the program, Indel_FS is not equivalent to FS. What tool did you annotate you vcf with to produce the Indel_FS annotation?

    Geraldine Van der Auwera, PhD

  • tinutinu Member Posts: 48

    Hi Geraldine,

    GATK was used to annotate the VCF and a particular variant the FILTER field has values 'Indel_FS,Indel_QD'.
    So would it work if I change ',' to ';' in the VCF ?

  • tinutinu Member Posts: 48

    Yes, I tried changed the FILTER field value from 'Indel_FS,Indel_QD' to 'Indel_FS;Indel_QD' and it worked

    Many Thanks

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