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Old 11-10-2014, 05:22 AM   #1
yuelincoln
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Location: hK

Join Date: Jun 2014
Posts: 5
Default How to deal with this problem? Reordersam treat bam file

##### ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Lexicographically sorted human genome sequence detected in knownSites.
##### ERROR For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs.
##### ERROR This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files.
##### ERROR You can use the ReorderSam utility to fix this problem: http://gatkforums.broadinstitute.org...ies-reordersam
##### ERROR knownSites contigs = [chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chrM, chrX, chrY, chr9]
##### ERROR ------------------------------------------------------------------------------------------
INFO 22:20:10,569 HelpFormatter - --------------------------------------------------------------------------------

This error was happend when i run BaseRecalibrator of the bam file.
I also have used ReorderSam.jar to re-order the bam file, but it still didn't work.
java -jar /usr/local/software/picard-tools-1.105/ReorderSam.jar I=./PET19_malformed.bam O=./PET19_reorder.bam REFERENCE=/home/george/alignment/gatk_resource/ucsc.hg19.fasta CREATE_INDEX=True
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