I download GnomAD vcf files in GRCh38 (hg19 remap). I want to convert this vcf in a table so i try to use VariantsToTable. But i have this error : The provided VCF file is malformed at approximately line number 10609: Duplicate allele added to VariantContext: C
line 10609 :
10 3101451 rs4881080 C C,T,G 191085017.71 PASS AC=237624,66,1;AF=9.99663e-01,2.77656e-04,4.20691e-06
I agree C is in REF and ALT colum but we can use VariantsToTable without check the integrity of vcf files?