Re: [Bio-bwa-help] unaligned read without read group

[Kurt H. <khe...@jh...>]

Hi Gilgi,

Use this version (your problem is fixed in it)

From: Heng Li [lh...@sa...]
Sent: Saturday, January 15, 2011 10:37 AM
To: Kurt Hetrick
Cc: James W. MacDonald; bio...@li...
Subject: Re: [Bio-bwa-help] RG:Z tag not added to unmapped reads in bwa-0.5.9rc1

Bug fixed at:

https://github.com/lh3/bwa

Heng

Best Regards,

Kurt


Message: 1
Date: Wed, 19 Jan 2011 18:35:40 +0200
From: "Gilgi Friedlander" <Gil...@we...>
Subject: [Bio-bwa-help] unaligned read without read group
To: <bio...@li....>
Message-ID: <4D3...@wi...>
Content-Type: text/plain; charset="us-ascii"

Hello,

I am using bwa to align Illumina reads. I used the -r option in order to specify the read group.
In the output sam file I have a read group only for the aligned reads. Reads that are not mapped (with '*' in the chromosome and position) don't have a read group.
In the downstream analysis I use GATK, which gives errors because of this. Any suggestions?

Thanks,
Gilgi