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Old 10-18-2011, 01:05 PM   #1
efoss
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Location: Seattle

Join Date: Jul 2011
Posts: 98
Default basic question about read groups

I have run into problems in which GATK complains that my bam file is malformed because it's missing read group information. I have fixed this by going back to the "sampe" step in bwa and adding a "-r" option and today for the first time I'm trying to fix this with PicardTools' "AddOrReplaceReadGroups" tool. But these tools take quite a long time to run. Would there be anything wrong with simply adding the read group information manually at the top of a sam file and then converting that sam file to a bam file? I guess I don't know if there is anything more to the read group than a line near the beginning of a sam file or whether instead adding read group information with a bwa tool or a PicardTools tool is doing something more involved (e.g. somehow embedding read group information in multiple places in the sam/bam file).

Thank you.

Eric
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