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problem with IndelRealigner, --disable_bam_indexing, and --nWayOut

dgscofielddgscofield Member
edited October 2012 in Ask the GATK team

Hi, I've run into what appears to be a bug in handling output in IndelRealigner. When specifying --nWayOut everything works, but when I add --disable_bam_indexing, it appears to be expecting --out instead?

##### ERROR A USER ERROR has occurred (version 2.1-13-g1706365): 
....
##### ERROR MESSAGE: Value for argument with name '--out' (-o) is missing.
Post edited by Geraldine_VdAuwera on

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