To build Platypus, simply un-pack the tar-ball and run the buildPlatypus.sh script provided: It requires only Python (>=2.6) and a C compiler to build these are standard on most linux and Mac OS distributions, and Platypus should build and run without problems for most people. Platypus is written in Python, Cython and C. Platypus will run on any input data in BAM format, but has only been properly tested on Illumina data. Duplicate read marking, local re-alignment, and variant identification and filtering are performed on-the-fly using a single command. Platypus can process large amounts of BAM data very efficiently, and can handle samples spread across multiple BAM files. It can identify SNPs, MNPs and short (less than one read length) indels, and larger (up to several kb deletions and maybe 200bp insertions) variants using local assembly. 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 has also been used to find somatic mutations in cancer, and mozaic mutations in human exome data. Platypus has been used to detect variants inhHuman, mouse, rat and chimpanzee samples, amongst others, and it should perform well on data from any diploid organism. It has not been tested with other mappers, but it should behave well. Platypus has been thoroughly tested on data mapped with Stampy and BWA. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. User forum and update notifications (Google group)Įxamples of how to run Platypus in different settings Nature Genetics (2014) doi:10.1038/ng.3036ĭownload the latest stable version of Platypus

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R.

Platypus full version