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
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
Comment