Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?