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Old 01-19-2011, 12:08 PM   #1
Location: il

Join Date: Jun 2010
Posts: 64
Default 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?

gfmgfm is offline   Reply With Quote
Old 01-20-2011, 04:10 AM   #2
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?
aleidenroth is offline   Reply With Quote
Old 01-20-2011, 05:49 AM   #3
Senior Member
Location: Boston

Join Date: Feb 2008
Posts: 693

you should join the bwa mailing list. already fixed a while ago.
lh3 is offline   Reply With Quote

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