Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data

Authors:  Andy Rimmer, Hang Phan, Iain Mathieson, Gerton Lunter, Gil McVean
   

Description

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. Platypus uses local realignment of reads and local assembly to detect variants. It is both sensitive and specific. Platypus can detect SNPs and short indels in low and high coverage data, and has been tested on whole-genome, exon-capture, and targeted capture data. Platypus is recommended for use with Stampy, but will also work well on data mapped with BWA. I have not tested it with other mappers, but believe it should behave well. Platypus has been used to detect variants in Human, Mouse, Rat, and Chimpanzee samples. The current version (0.2.3) should perform well on data from any diploid organism.
Capabilities Platypus reads data from BAM files, and outputs a single VCF file containing a list of identified variants, and genotype calls and likelihoods for all samples. It can identify SNPs and short (less than one read length) indels, and has experimental support for larger (up to ~1kb deletions and maybe ~200bp insertions) variants using local assembly. Platypus can process large amounts of BAM data very efficiently, and can handle samples spread across multiple BAM files.
   
Reference:  A Platypus paper is in the pipeline. For the time being, if you use Platypus, please reference this site, with the following text: Rimmer A, Mathieson I, Lunter G, McVean G, (2012) Platypus: An Integrated Variant Caller (www.well.ox.ac.uk/platypus).
   

Download Platypus:

You can download the latest stable version of Platypus here. To build Platypus, simply un-pack the tar-ball and run the buildPlatypus.sh script. Platypus has no dependencies other than Python. A README file is included in the tar-ball.
Contact:  Bug reports, comments, and feature requests can be sent to Andy Rimmer