Hi GATK team,
I tried to subset vcf file using SelectVariants, but I got the error: The following invalid GT allele index was encountered in the file: "0. The subsetted vcf has only header lines and record header, no variant site records. I then used ValidateVariants to check the vcf file, and things seem ok. I am struggling to understand what's wrong with my vcf. Can you please help? :)
I tried to subset vcf file using SelectVariants, but I got the error: The following invalid GT allele index was encountered in the file: "0. The subsetted vcf has only header lines and record header, no variant site records. I then used ValidateVariants to check the vcf file, and things seem ok. I am struggling to understand what's wrong with my vcf. Can you please help? :)