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SelectVariants V4 TribbleException Contig chr1 does not have a length field
I indexed my VCF file with GATK V126.96.36.199 IndexFeatureFile, then ran GATK V188.8.131.52 SelectVariants on it, and I got an exception:
htsjdk.tribble.TribbleException: Contig chr1 does not have a length field.
When I run the same VCF using GATK V3 SelectVariants, it works.
As far as I know, ##contig entries in the VCF header should NOT have a length in them.