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Old 01-19-2011, 01:08 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?

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