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My question could seems like here but, the answer didn't help me.
I am using VariantFiltration over a VCF file which is generated directly after UnifiedGenotype under GenomeAnalysisTK-2.3-9-ge5ebf34.
The error I am facing is
##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 126: there aren't enough columns for line 70 (we expected 9 tokens, and saw 1 )
Line number 126 is as following,
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT m1016ROUa.40287 m1023ROGa.40244 m1042ujba.40261 m1069FXFa.49470
And actually indeed it is the header of VCF file ! Should I re-run my samples ?!!