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Error details: The contig order in variant and reference is not the same after running SortVCF

Hi GATK team
I am trying to compare variants called with GATK 3.7 and samtools mpileup. I have used the same reference genome files, same bam files.
Right now, I just wanted to pit everything in the same format and to a table to inspect and filter variants.
When running VariantsToTable I get the following error message
ERROR MESSAGE: Input files variant and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information. Error details: The contig order in variant and reference is not the same; to fix this please see: (https://www.broadinstitute.org/gatk/guide/article?id=1328), which describes reordering contigs in BAM and VCF files..
I have checked both links and used picard.jar SortVcf with the correct reference dictionary. This runs through without any error. Now using the newly sorted vcf file as input for VariantsToTable I still get the same error message which seems strange to me
Could it be that I am missing anything here?

Answers

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