I'm using RVboost to perform some RNAseq variant calling. I've done some tophat2 and then using the .bam file I'm using RVboost, but when I use it I get: RNA bam file : accepted_hits_picard.bam doesn't have Read Group Information, Read Group is necessary in the BAM to run the pipeline.

So I tried using picard tools as described below. But RVboost keeps sending me back the same error.
I have seen how the header is changed by adding two lines corresponding to @RG, so everything seems to be going as expected.

java -jar AddOrReplaceReadGroups.jar INPUT=/local/RNAseq_variant/Raw_data/Panc042_PDAC_PRITUM_Px00/FastQ_files__RNASeq_data/tophat_out/accepted_hits.bam OUTPUT=/local/RNAseq_variant/Raw_data/Panc042_PDAC_PRITUM_Px00/FastQ_files__RNASeq_data/tophat_out/accepted_hits_picard.bam RGID=Unknown RGCN=unknown RGDS=unknown RGPI=41 RGPL=illumina RGLB=LaneX RGPU=NONE RGSM=AnySampleName

¿Do you have any clue about if I may be missing something during the the use of AddOrReplaceReadGroups?


Best Answer


  • Thanks I already solved the problem. it wasn't a problem of AddOrReplaceReadGroups.jar

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