Run Picard tools and collate multiple metrics files
Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data files such as BAM and VCF. I needed to check the quality of thousands of BAM files, so I created a Bash script called picardmetrics. It runs 10 of the Picard tools on a BAM file and easily collates all of the generated metrics files into a single table. I also include utility scripts for generating the reference files required for Picard.