I cannot find this in the manual or online (though admittedly I'm not sure what exactly I should be searching for)
Simple question: my input fasta and vcf both have "chr22" (for example) yet GATK insists on outputting the new fasta as chromosome ">1"
Is there a GATK-native way to stop this behavior or do I just need to do a sed replace after the fact?
Also just curious why this is the default?--seems counterintuitive.
Thanks for any help!
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