Cancer Panel Analysis Pipeline (CPAP) Release!

Cancer Panel Analysis Pipeline (CPAP) is an automatic pipeline for the analysis of Ion AmpliseqTM Cancer Panel target sequencing datasets generated by the Life Technologies Ion Personal Genome Machine™(PGM™) sequencer. High throughput sequencing of cancer panel by using the bench top Ion Torrent sequencer is the most powerful application for clinical genetic testing and screening SNPs. Although the Ion Torrent sequencing machine preinstalled a Torrent Suite Software with a variant caller plugin for identifying variants from the sequencing result of each sample, no additional tools are available for the comparative analysis and visualization of multiple datasets.

CPAP uses both XLS and VCF,standard output files from the variant caller plugin of Torrent Suite Software, to generate a distribution map of genetic variants amongst all samples in a circular diagram by Circos. The circular diagram is hyper-linked to a Dynamic HTML Table that allows the users to identify variants of interest by using different filtering items such as chromosome, gene symbol, amplicon id or sample id.

CPAP can also provide additional information of the identified variants by linking to an integrated SQLite database complied from population-related databases(dbSNP and 1000 Genomes Project), cancer-associated database(COSMIC) and functional prediction database of human non-synonymous SNPs(dbNSFP).
Besides, external links to the UCSC Genome Browser were embedded in the output pages of CPAP, which provides a convenient way for inspecting variants from each sample and informative tracks on the UCSC Genome Browser at the same time. CPAP only takes 17 minutes to complete a comparative analysis of 500 datasets by using 8 CPU cores. As far as we know, CPAP is the only web-based application for the analyses of multiple sequencing datasets generated from the ion Ampliseq™ Cancer Panel.

Huang PJ, Yeh YM, Gan RC, Lee CC, Chen TW, Lee CY, Liu H, Chen SJ, Tang P. CPAP: Cancer Panel Analysis Pipeline. Hum Mutat. 2013 Jul 24. doi: 10.1002/humu.22386.