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Contest error: mismatched contigs

Hello,

I've downloaded bams from dbGaP, that were aligned to grch37. GATK Contest tool is saying mismatched contigs when using hg19.

  • Is there a different reference I should use, if yes, which one?
  • If I replace the header of the downloaded bams with a header from an hg19 bam, is that acceptable?
    It seems like the tool might only look at the header to make sure everything is ok?

Thanks!


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