missing read groups for unaligned reads

gfmgfm · 01-19-2011, 01:08 PM

Hi everyone,

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 am getting read groups 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 how to overcome this?

Thanks

aleidenroth · 01-20-2011, 05:10 AM

I have the same problem, I also use bwa -r for alignment.

When I re-run TableRecalibrate with the added parameter

--default_read_group name_of_my_read_group

it seems to work and ignores the unmapped reads. However, I'm not sure this will cause any trouble in downstream analysis?

lh3 · 01-20-2011, 06:49 AM

you should join the bwa mailing list. already fixed a while ago.

https://github.com/lh3/bwa

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01-19-2011, 01:08 PM	#1
gfmgfm Member Location: il Join Date: Jun 2010 Posts: 64	missing read groups for unaligned reads Hi everyone, 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 am getting read groups 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 how to overcome this? Thanks

01-20-2011, 05:10 AM	#2
aleidenroth Junior Member Location: Nottingham, UK Join Date: Nov 2009 Posts: 8	I have the same problem, I also use bwa -r for alignment. When I re-run TableRecalibrate with the added parameter --default_read_group name_of_my_read_group it seems to work and ignores the unmapped reads. However, I'm not sure this will cause any trouble in downstream analysis?

01-20-2011, 06:49 AM	#3
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	you should join the bwa mailing list. already fixed a while ago. https://github.com/lh3/bwa