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Old 01-31-2013, 12:57 AM   #1
FGponce
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Location: New Zealand

Join Date: Dec 2011
Posts: 9
Default Trouble with RG line

Hi,
am trying to add RG line to a Sam made after bwa alignment prior to GATK.

This is the command:
bwa sampe -f OD.sam -r "@RG\tID:<ODexome>\tLB:<ODexome>\tSM:<ODexome>\tPL:ILLUMINA" hg19 OD_R1.sai OD_R2.sai SampleR1_001.fastq SampleR2_001.fastq

BUT get this error!

[bwa_sai2sam_pe] malformated @RG line

Any ideas?

Cheers,

FGP

Last edited by FGponce; 01-31-2013 at 10:41 PM.
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