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error using somatic indel detector

EarendilEarendil Posts: 2Member
edited January 2013 in Ask the GATK team

hello every one please i got this error while running this command

elendin@elendin-HP-Pavilion-dv6700-Notebook-PC:~/analysis of rnaseq bamfiles$ java -jar GenomeAnalysisTK.jar -R VitisVinifera.fasta -T SomaticIndelDetector -o indels.vcf -verbose indels.txt -I:normal wt.bam -I:tumor newmut.bam

MESSAGE: SAM/BAM file SAMFileReader{/home/elendin/analysis of rnaseq bamfiles/newmut.bam} is malformed: Read HWI-ST132_0461:3:2201:1211:140854#GTCCTA is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use to fix this problem

ERROR ------------------------------------------------------------------------------------------

how can i add the missing read group for HWI-ST132_0461:3:2201:1211:140854#GTCCTA or define it in the header.

Post edited by Geraldine_VdAuwera on


  • ebanksebanks Broad InstitutePosts: 698Member, Administrator, Broadie, Moderator, Dev admin

    This is addressed in the documentation on this forum. The error you posted specifically asks you not to post this problem to the forum because it's something you can easily fix just by reading the docs that our team has spent a lot of time preparing.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • TomAmesTomAmes Posts: 6Member

    FYI, that link redirects to the main GATK site, and there does not seem to be any way to find the wiki entry that contains the documentation.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,567Administrator, Dev admin

    We changed from the wiki to this website, but old versions of the code still produce old links.

    FYI, what you're looking for is the first link you get if you use the search box with the terms "ReplaceReadGroups"...

    Geraldine Van der Auwera, PhD

  • TomAmesTomAmes Posts: 6Member

    Thanks, Geraldine. (FWIW, I'm not having the problem mentioned above--was just pointing out that the solution was not at the link given to the OP).

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