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

Join Date: Apr 2010
Posts: 143
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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:

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