Tagged with #reference error
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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?

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With the following command line: java -jar GenomeAnalysisTKLite.jar -T CoverageBySample -I NGS0237-0014L_S5.ref_21563.bam -R 21563.fa -L 21563 -o out

I get

INFO 11:37:18,112 HelpFormatter - --------------------------------------------------------------------------------- INFO 11:37:18,113 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-13-g0f021e6, Compiled 2012/10/12 17:51:55 INFO 11:37:18,113 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:37:18,113 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 11:37:18,114 HelpFormatter - Program Args: -T CoverageBySample -I NGS0237-0014L_S5.ref_21563.bam -R 21563.fa -L 21563 -o out INFO 11:37:18,114 HelpFormatter - Date/Time: 2012/10/24 11:37:18 INFO 11:37:18,114 HelpFormatter - --------------------------------------------------------------------------------- INFO 11:37:18,114 HelpFormatter - --------------------------------------------------------------------------------- INFO 11:37:18,117 GenomeAnalysisEngine - Strictness is SILENT

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.1-13-g0f021e6):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: Invalid command line: Failed to load reference dictionary
ERROR ------------------------------------------------------------------------------------------

My reference sequence is a fasta file as I believe is specified in the documentation and has no non-standard bases.

What's wrong?

Thanks for your help (I'm new to using GATK)