Tagged with #incompatible contigs
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Created 2013-08-23 14:16:01 | Updated | Tags: realignertargetcreator realignment
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Hello

I am currently trying to run the RealignerTargetCreator on some bam files which were aligned to hg19 howver am getting this error `ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but different lengths:

ERROR contig known = chrM / 16571
ERROR contig reference = chrM / 16569.`

After some initial investigation I found that the supplied hg19 reference genome which was being used for mapping was using rCRS mtDNA. other then realigning to a different build of hg19 is there any way to easily fix this problem through GATK?


Created 2013-08-14 15:39:16 | Updated | Tags:
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ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
ERROR contig reads = chrM / 16569
ERROR contig reference = chrM / 16571.

I'm trying to run some tests and can't because I get this message that my reference is not the same as the input file, even though I've been assured that it is. Is there a way around this? I'm new to this, so step-by-step details would be appreciated, thanks

Rauh Lab