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!