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.

error using somatic indel detector

EarendilEarendil Posts: 2Member
edited January 2013 in Ask the 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 http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups 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. thanks

Post edited by Geraldine_VdAuwera on

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