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how to add read groups in BAM file of 454 sequencing data using PICARD for further downstream processing in GATK?
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I have never worked with 454 data, but I am still guessing that the BAM file would be similar to what you'll get for say HiSeq data. If that's the case, you could use the "AddOrReplaceReadGroups" module in picard tools to add read groups to your bam file. See the following link for more details:
e.g
java -jar AddOrReplaceReadGroups.jar INPUT=Input_file.bam OUTPUT=Read_group_added_file.bam RGID=ReadGroupID RGLB=ReadGroupLibrary RGPL=454Sequencing RGPU=PlatformUnit RGSM=Sample
I hope this helps.
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