How to get a report like stuff of a bam file how many percent of the exons are coverred?

Question

[Clark_BioMorgan]

Dear Collegues,

Lets say I have a miseq run and have the .bam file from the squencer and I would like to know how many percent of the exons (specific genes) are coverred in these .bam files?

Is it possible?

Thanks in advance

Answer 1

[WouterDeCoster]

You can use Picard HsMetrics for that.

[ATpoint]

Or you might consider to use the search function because this question has been asked like a hundred times before ;-)