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Exome Capture Metrics GVA2017

Exome Capture Metrics GVA2017

Evaluating capture metrics

There are many ways to measure sequence capture.  You might care more about minimizing off-target capture, to make your sequencing dollars go as far as possible.  Or you might care more about maximizing on-target capture, to make sure you get data from every region of interest.  These two are usually negatively correlated.

Using Picard's "CalculateHsMetrics" function to evaluate capture

Here is a link to the full documentation.

To run the program on Lonestar, there are three prerequisites: 1) A bam file and 2) a list of the genomic intervals that were to be captured and 3) the reference (.fa).  As you would guess, the BAM and interval list both have to be based on exactly the same genomi