Base quality score recalibration
Thank you for the great description on detecting SNPs from RNA-seq data.
I am using RNA-seq data to call SNPs but I don't have any known set of SNPs for my species. I am now in the step to recalibrate quality score but when I try to run the command, it gives an error that I need to provide a set of known SNPs. I understand the reason for this because the tool is considering any mismatch to be an error and providing a set of known SNPs, will tell the software to skip these positions but does it mean that I should skip BQSR for my samples?
Thanks for any hint on this.