Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

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

dgscofielddgscofield Posts: 0Member
edited October 2012 in Ask the 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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