An updated version of Pindel is available for download.

Pindel is a program that detects short indels and complex structural variants (large deletions, inversions, tandem duplications, mobile element insertions and translocations) from next-generation sequence data using pattern growth.

It takes either extracted reads (using sam2pindel or bam2pindel.pl) or multiple bam files as input. A pindel2vcf converter is provided to report variant calls in VCF format.

The source code for Pindel is available on GitHub, and pre-built packages for Ubuntu 10.04 systems are available from The Genome Institute. For installation instructions, see the Pindel project page.