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Input files known and reference have incompatible contigs.

igorigor New YorkMember ✭✭

I am getting the following error from RealignerTargetCreator in GATK 3.6:

##### ERROR MESSAGE: Input files known and reference have incompatible contigs. Please see https://www.broadinstitute.org/gatk/guide/article?id=63for more information. Error details: The contig order in known 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..
##### ERROR   known contigs = [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY]
##### ERROR   reference contigs = [chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY]

The known VCF file was sorted with Picard SortVcf as GATK suggests, so this should not be happening.

I manually checked all my files and they all start with chr10. I checked the VCF file (known) and it starts with chr10 in both the header and in the actual file. I also checked genome.fa, genome.dict, genome.fa.fai, and the BAM file. They all start with chr10. Why is GATK telling me that the known contigs start with chr1? Where is it getting that order?

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