How to get coverage ratio?

Question

[897598644]

Dear colleagues:

I have got whole exome sequencing data of dozens of samples. I want to know how we can get the exome data capture quality index of coverage ratio.

Any help that can help me to understand the question would be appreciated.

Best!

Answer 1

[Danielk]

Sounds like a job for Picard CalculateHsMetrics.

Run it on each bam file, then check the column PCT_SELECTED in the output metrics file for each sample.

[897598644]

Are there any examples of command lines to show how to achieve it?

[Danielk]

It's something like

java -jar CalculateHsMetrics.jar INPUT=in.bam METRICS=metrics.txt

but do check the details of the syntax on their website, it changed recently so the above might not be correct (but correct-ish).

[MAPK]

What would be the metrics.txt file look like?