Question: Calculating bam/fastq metrics
gravatar for ebrown1955
3.8 years ago by
United States
ebrown1955300 wrote:

Hi All, I just got a few QC questions back from my sequencing center, as they are trying to streamline the sequencing process for our next batch of samples.

The questions are:
1) What was the average duplication rate?
2) What was the % On Target ?
3) What was the uniformity of the reads on target?

I'm not really sure what tools I should use to calculate these metrics. If I can calculate the breakpoints for regions with coverage > (say 30), and compare this to the targets, I can calculate the percent on target.

I'm not sure what to do about average duplication rate, and uniformity of targets primarily. Any easier solutions to percent on target would be appreciated as well!

bam fastq exome sequencing • 1.4k views
ADD COMMENTlink written 3.8 years ago by ebrown1955300

UPDATEl: I actually used CalculateHSMetrics from the PicardTools suite for percent on target.

ADD REPLYlink written 3.8 years ago by ebrown1955300
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