VariantFiltration - FORMAT Required

wukhanwukhan PakistanMember


Dear GATK Community,

I am running VariantFiltration on my VCF file that has no FORMAT and SAMPLE column and it gives me the following error:

ERROR MESSAGE: Your input file has a malformed header: The FORMAT field was provided but there is no genotype/sample data

Is there any way to run VariantFiltration by-passing this error or is it really very necessary to have a VCF file with this FOMRAT and SAMPLE information / column?




  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Waqas,

    I don't think it is necessary to have those, but if you have the COLUMN names and no information in those columns, that might cause an error. How did you prepare the VCF?


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