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Old 11-08-2013, 05:56 AM   #2
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Location: France

Join Date: Apr 2010
Posts: 143

I use a different read-group for each pair of (paired-end) fastq, even if they belong to the same lane/lib/sample etc...: in the end I can find the FASTQ from a given SAM-Record. My scripts look like this:

(bwa...) -r "@RG	ID:${pair.generateId}	LB:${pair.sample.lib}	SM:${}	PL:ILLUMINA	PU:${pair.lane}" \
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