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Old 11-10-2011, 01:00 AM   #3
alexbmp
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Location: Seoul, South Korea

Join Date: Oct 2011
Posts: 30
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I used picard AddOrReplaceReadGroups.jar on this problem.

I think samtools also can add (actually, replace: by samtools reheader) read groups to your bam file.

For example:
Quote:
java -Xmx4g -jar /home/lab/bin/picard/AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT VERBOSITY=ERROR SO=unsorted INPUT=sample.cat.pic OUTPUT=sample.rga.bam RGPL=illumina RGLB=sm_1110 RGPU=barcode_1110 RGSM=sample_1110
Any other ideas?

Last edited by alexbmp; 11-10-2011 at 01:20 AM.
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