GATK BaseRecalibrator complaining about sort order of VCF file that is sorted correctly

lstbllstbl CU BoulderMember
edited August 2016 in Ask the GATK team

I am running GATK's BaseRecalibrator with 2 input .vcf files with known SNPs.

Both of these VCF files have been sorted using picardtools SortVcf

Upon visual inspection, both VCF files are sorted correctly--i.e. same as the genome fasta file.

However, when I run BaseRecalibrator, I get an error that one of the VCF files is not sorted the same as the reference genome. The list of chromosomes that GATK dumps out is indeed not sorted the same--for some reason all the chrX contigs are stuck at the end instead of after the mitochondrial chromosome like they are in the reference fasta and the original VCF files.

I've attached the full output error as well as the header of the problematic VCF file

Thanks for any help!

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