THetA DNAnexus Applet

This DNAnexus applet provides a containerized version of THetA (Tumor Heterogeneity Analysis) for estimating tumor purity and subclonal population frequencies from next-generation sequencing data.

Overview

THetA is a tool for analyzing tumor heterogeneity using next-generation sequencing data. This applet provides a Docker-based implementation that can be run on the DNAnexus platform.

Requirements

• DNAnexus account with appropriate permissions
• Docker image: jbkirkland/theta:latest

Input Parameters

Required

• interval_count_file: File containing interval counts

Optional

• normal_interval_count_file: File containing normal interval counts
• tumor_interval_count_file: File containing tumor interval counts
• tumor_allele_count_file: File containing tumor allele counts
• normal_allele_count_file: File containing normal allele counts
• num_chains: Number of MCMC chains to run (default: 3)
• num_chains_to_use: Number of chains to use in the analysis (default: 3)
• num_iterations: Number of iterations per chain (default: 1000)
• burn_in: Number of burn-in iterations (default: 100)
• max_solutions: Maximum number of solutions to return (default: 100)

Output

• results: Results file from THetA analysis (*.results)

System Requirements

• Instance Type: azure:mem2_ssd1_x8
• Timeout: 48 hours

Usage

The applet can be run using the DNAnexus command line tools:

dx run theta -iinterval_count_file=<file_id> [optional parameters]

Docker Image

The applet uses the Docker image: jbkirkland/theta:latest

License

[Add appropriate license information]