This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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.