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FastaAlternateReferenceMaker output contig names?

David_RDavid_R United StatesMember

Is there any way to make the output from FastaAlternateReferenceMaker not rename the contigs?

I'm running a pipeline that (theoretically) has worked with previous verions of GATK ( but is now broken because FastaAlternateReferenceMaker renames contigs.

I can fix with a one-liner but wondered if there was a native GATK option?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited August 2017


    I suspect the tool does that on purpose so you don't get confused between the original reference and new reference. I don't think there is any way to change the default behavior.

    You will indeed have to make the fix yourself if you want.


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