Updated hyperlinks on the 2015 January 26th; please comment if you find any more dead links.
Picard is a suite of Java-based command-line utilities that manipulate SAM/BAM files. Currently, I'm analysing some paired-end libraries and I wanted to calculate the average insert size based on the alignments; that's how I found Picard. While reading the documentation I realised that Picard has a lot more to offer and hence I'm writing this post to look into specific tools that I thought would be useful.
To get started, download Picard and an alignment (whole genome shotgun sequencing) from the 1000 genomes project that we can use to test Picard: