How To Compute Coverage From A Picard Metrics Output File.

Question

[ndvenkova]

Hello all, I have a file with hybrid metrics from aligned exome (X20) data(e.g Genome_size, Bait_territory, Target_territory, Bait_design_efficiency, Total_reads, Pf_reads....etc). How do i calculate the coverage from the metrics in the file; which metrics should i use? Thanks.

Answer 1

[Dan D]

You'll want to use the CalculateHSMetrics tool. You'll have to reformat your bait and target info files into the BED format that Picard wants, but once you do you'll get very detailed output.

Link to documentation for the tool