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  • Count error rate of sam file

    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)

    Meanwhile,is there any easy way to combine the CIGAR and MD strings to to get the insertion,indel and mismatch base of each read aligned to the reference genome.

    Any answer is appreciated.

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