I have aligned the fastq file to the reference genome and got a sam file. I know use "samtools stats" can get "error rate" of the sam file.
Is there any document shows how the error rate is calculated from the sam file? (since I want to seperately calculate the error rate of every read in the sam file instead of the average of the whole file)
I am really confused how they deal with softclips and hardclips when calculating the error rate.
Any answer is appreciated.