GATK CombineVariants complains the contig order in the VCF files

cr517cr517 CambridgeMember

I have called variants on two strains of C. elegans separately. I now want to merge the VCF files into one using the following code:

  • Create a sequence dictionary of the reference sequence
  • Sort the VCF files with Picard
  • Merge the sorted VCF files using GATK


picard CreateSequenceDictionary \
    REFERENCE=c_elegans.PRJNA13758.WS263.genomic.fa \

picard SortVcf INPUT=strain1.vcf \
    OUTPUT=strain1sorted.vcf \

picard SortVcf INPUT=strain2.vcf \
    OUTPUT=strain2sorted.vcf  \     

GATK --analysis_type CombineVariants \
    -R c_elegans.PRJNA13758.WS263.genomic.fa \
    --variant strain1sorted.vcf \
    --variant strain2sorted.vcf \
    -o all.vcf \
    -genotypeMergeOptions UNIQUIFY

The last command gives me the following error message:

ERROR MESSAGE: Input files variant and reference have incompatible contigs. Please see for more information. Error details: The contig order in variant and reference is not the same; to fix this please see: (,  which describes reordering contigs in BAM and VCF files..
##### ERROR   variant contigs = [I, II, III, IV, MtDNA, V, X]
##### ERROR   reference contigs = [I, II, III, IV, V, X, MtDNA]

But I have sorted the VCF files using Picard, so I don't know what else to do.

Your help is appreciated.

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