Error when using bwa sampe -r option

[yjx1217]

Hello,

I was trying to use -r option to assign read group information to the sam output of bwa, but it fails every time...Does anybody know why? Thx

I called bwa sampe command in a perl script like:
system "/users/jy16/Programs/bwa-0.6.0/bwa sampe ‐r '\@RG\\tID:test1\\tSM:$i\\tLB:$i\\tPL:Illumina' bf1.scaffold_1.fasta $i.scaffold_1.read1.sai $i.scaffold_1.read2.sai ./Maq_reads/$i.scaffold_1.read1.trimmed.fastq ./Maq_reads/$i.scaffold_1.read2.trimmed.fastq >$i.scaffold_1.sam";

the error message is like this>>

[bns_restore_core] fail to open file '‐r.ann'. Abort!
sh: line 1: 18616 Aborted /users/jy16/Programs/bwa-0.6.0/bwa sampe ‐r '@RG\tID:test1\tSM:1\tLB:1\tPL:Illumina' bf1.scaffold_1.fasta 1.scaffold_1.read1.sai 1.scaffold_1.read2.sai ./Maq_reads/1.scaffold_1.read1.trimmed.fastq ./Maq_reads/1.scaffold_1.read2.trimmed.fastq > 1.scaffold_1.sam

[SharonCox]

I am using bwa 0.6.2 and I am having the same problem....did you fix it?
The -r option in my version of bwa is no longer present when using the "bwa sampe" command

[yjx1217]

I am using bwa 0.6.2 and I am having the same problem....did you fix it?
The -r option in my version of bwa is no longer present when using the "bwa sampe" command

Hi Sharon,

While I did not remember exactly, I thought I used picardtools to get the problem fixed.

You can check>>

http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGroups

Hope this helps!

Best,
yjx1217