BWA sampe malformed @RG line

[mcgreevy]

Coming into work today code that was working all last week now is giving problems. I have fastq files, i align them using bwa aln then create sam files using the following:

~/bwa-0.5.9/bwa sampe -r ~/resources/genomes/ucsc.hg19.fasta @saiA[$i] @saiB[$i] @fastqA[$i] @fastqB[$i] > @saiA[$i].sam

I get the error

[bwa_sai2sam_pe] malformated @RG line

Any ideas why this would be happening?

[Rhizosis]

I couldn't give you any specific solutions, but it looks like the readsgroups have not been formatted correctly.

http://bio-bwa.sourceforge.net/bwa.shtml

In the argument listing:
"-r STR Specify the read group in a format like ‘@RG\tID:foo\tSM:bar’. [null]"

Maybe quote the readgroup arguments?

[mcgreevy]

thanks it was a silly error -r doesn't specify the reference genome it specifies the read group IDs.. thanks for the reply. everything working now

[Rhizosis]

Good to hear! Good luck!

[prasadg]

thanks it was a silly error -r doesn't specify the reference genome it specifies the read group IDs.. thanks for the reply. everything working now

Hello,

I am having the same problem. how did you specify the -r ?

This is my sample id : @HWI-ST741:2040TEJACXX:8:1101:1107:1901 1:N:0: BC=ACGTAA SAMPLE=1 LENGTH=64 MEAN_QUAL=38.6

how should i try the code for this header?

Thanking in anticipation.

[dpryan]

Hello,

I am having the same problem. how did you specify the -r ?

This is my sample id : @HWI-ST741:2040TEJACXX:8:1101:1107:1901 1:N:0: BC=ACGTAA SAMPLE=1 LENGTH=64 MEAN_QUAL=38.6

how should i try the code for this header?

Thanking in anticipation.

That's not a read group, that's the name of an individual read (along with it's barcode and other information that's unrelated to a read group). The two are unrelated. Check out the SAM specification (or search the forum) for further information.

[sigma]

Hi,

It's an old post but i have a problem with -r option of BWA.
How to use this option ?
Actually a string is necessary but which one to put ?

advance thanks,
Siva

[dpryan]

Hi,

It's an old post but i have a problem with -r option of BWA.
How to use this option ?
Actually a string is necessary but which one to put ?

advance thanks,
Siva

Yes, a string is required. Exactly what that string is is entirely dependent on what information you want associated with things. There is an example up-thread in the second post (obviously, you would want to change "foo" and "bar" into something meaningful for you). You can also add more information, such as platform.

[sigma]

bwa sampe -n 1 -r @RG\tID:NAME\tSM:NAME -f ...

I still have the error : [bwa_sai2sam_pe] malformated @RG line

[Rhizosis]

Hi,

It's an old post but i have a problem with -r option of BWA.
How to use this option ?
Actually a string is necessary but which one to put ?

advance thanks,
Siva

Please check out the options on this page:
http://linux.die.net/man/1/bwa

-r is meant for readgroup (RG) filtering and 'foo' in the proposed syntax can be used to only use RG's which you so desire to use in the alignments

[sigma]

It's working thanks to dpryan & Rhizosis.
I've forgotten to put '

[Rhizosis]

It's working thanks to dpryan & Rhizosis.
I've forgotten to put '

Glad you got it working, you had me wondering there for a second!
Good luck