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BAM header using BWA-MEM in galaxy compared with GATK resource bundle (hg38)


I am trying to perform CollectSequencingArtifactMetrics but I'm getting an error of the dictionary sizes.
Long story short, I performed BWA-MEM using hg38 in Galaxy Project ( and now I'm using hg38 provided in the GATK resource bundle ( The problem is that the header for the bam files generated from the BWA-MEM in Galaxy are different from the GATK reference genome fasta header (Homo_sapiens_assembly38.fasta).

Is there any way to solve this without remapping with GATK reference genome? Could I somehow edit the BAM header to match the GATK one?

Thanks! Joan

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