Question: How samtools calculate error rate
gravatar for jianzheng934963534
6 months ago by
jianzheng9349635340 wrote:

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.

sequencing samtools • 528 views
ADD COMMENTlink modified 6 months ago by Devon Ryan76k • written 6 months ago by jianzheng9349635340
gravatar for Devon Ryan
6 months ago by
Devon Ryan76k
Freiburg, Germany
Devon Ryan76k wrote:

samtools adds up the number of mismatches (from the NM auxiliary tag) and divides that by the number of aligned bases. Soft and hard-clipped bases wouldn't be included, since they aren't aligned.

ADD COMMENTlink written 6 months ago by Devon Ryan76k
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