bwa mem -R option

dakin · 05-02-2013, 08:13 AM

Trying to use bwa mem with the -R option to add read group headers to the alignment output in one step, but it keeps coming back with the error:

[E::bwa_set_rg] no ID at the read group line

Below was what I tried for paired-end reads and then for all single reads:

bwa mem -aM -R @RG\tID:Seq01p\tSM:Seq01\tPL:ILLUMINA\tPI:330 Refgen Seq01pair1.fastq Seq01pair2.fastq > Seq01pairs.sam

bwa mem -aM -R @RG\tID:Seq01a\tSM:Seq01\tPL:ILLUMINA\tPI:330 Refgen Seq01all.fastq > Seq01all.sam

If I take out the entire -R option, bwa mem appears to run just fine. I suppose I can always add the read group header on later with Picard or samtools, but it would be nice to add it now....

Wondering if there is something wrong with my read group ID line? Has anyone else successfully run bwa mem with the -R option and what did you use?

Richard Finney · 05-02-2013, 08:32 AM

I"m not sure but try quotes for your mem argument ...

bwa mem -aM -R "@RG\tID:Seq01p\tSM:Seq01\tPL:ILLUMINA\tPI:330" Refgen Seq01pair1.fastq Seq01pair2.fastq > Seq01pairs.sam

dakin · 05-02-2013, 08:42 AM

Thanks for the quick (and correct!) response - I tried it with the quotes, and it worked!

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05-02-2013, 08:13 AM	#1
dakin Junior Member Location: US Join Date: Dec 2009 Posts: 3	bwa mem -R option Trying to use bwa mem with the -R option to add read group headers to the alignment output in one step, but it keeps coming back with the error: [E::bwa_set_rg] no ID at the read group line Below was what I tried for paired-end reads and then for all single reads: bwa mem -aM -R @RG\tID:Seq01p\tSM:Seq01\tPL:ILLUMINA\tPI:330 Refgen Seq01pair1.fastq Seq01pair2.fastq > Seq01pairs.sam bwa mem -aM -R @RG\tID:Seq01a\tSM:Seq01\tPL:ILLUMINA\tPI:330 Refgen Seq01all.fastq > Seq01all.sam If I take out the entire -R option, bwa mem appears to run just fine. I suppose I can always add the read group header on later with Picard or samtools, but it would be nice to add it now.... Wondering if there is something wrong with my read group ID line? Has anyone else successfully run bwa mem with the -R option and what did you use?

05-02-2013, 08:32 AM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	I"m not sure but try quotes for your mem argument ... bwa mem -aM -R "@RG\tID:Seq01p\tSM:Seq01\tPL:ILLUMINA\tPI:330" Refgen Seq01pair1.fastq Seq01pair2.fastq > Seq01pairs.sam

05-02-2013, 08:42 AM	#3
dakin Junior Member Location: US Join Date: Dec 2009 Posts: 3	Thanks for the quick (and correct!) response - I tried it with the quotes, and it worked!