Platypus

Description

platypus website  

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. 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 has been thoroughly tested on data mapped with Stampy and BWA. It has not been tested with other mappers, but it should behave well. 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 also been used to find somatic mutations in cancer, and mozaic mutations in human exome data.

Required Modules

Serial

• gcc/5.2.0
• platypus

System Variables

• HPC_PLATYPUS_DIR - installation directory

Citation

If you publish research that uses platypus you have to cite it as follows:

Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R. F. Twigg, WGS500 Consortium, Andrew O. M. Wilkie, Gil McVean, Gerton Lunter. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.