TRAPD | Burden testing against public controls | Genomics library

TRAPD is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. TRAPD has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However TRAPD build file is not available. You can download it from GitHub.

Finding genes associated with Mendelian disorders can often be challenging. While some disorders are amenable gene discovery using family-based analyses (e.g., linkage or segregation), other disorders may be very challenging for a number of reasons (see Guo et al., AJHG. 2016. PMID: 27545677). One approach to identify genes associated with Mendelian disorders is to use burden testing, where the aggregate burden of rare protein-altering variants in each gene is tested against a set of suitable controls. While one may sequence a set of control samples or have control sample sequencing readily available, this is often too expensive and unavailable. Here, we provide a simple-to-use program called TRAPD (Testing Rare vAriants using Public Data) that allows for burden testing against publicly-available summary level data (e.g., ExAC or gnomAD). We have had a number of users ask us about how to filter their data. We refer users to our paper. Filtering data for parameters such as variant quality are dependent on your data and likely will need to be calibrated. Our paper outlines how we did this for our samples and outlines some general approaches. However, there is no one-size-fits-all approach. Requirements: TRAPD is written in Python and R. For Python, it is recommended to use Python version 2.7. For R, any version 2.+ should be okay. NOTE: As of 10/8/2019, TRAPD no longer required pybedtools.