hipFG: High-throughput harmonization and integration pipeline for functional genomics data

Abstract

SummaryPreparing functional genomic (FG) data with diverse assay types and file formats for integration into analysis workflows that interpret genome-wide association and other studies is a significant and time-consuming challenge. Here we introduce hipFG, an automatically customized pipeline for efficient and scalable normalization of heterogenous FG data collections into standardized, indexed, rapidly searchable analysis-ready datasets while accounting for FG datatypes (e.g., chromatin interactions, genomic intervals, quantitative trait loci). Availability and ImplementationhipFG is freely available at https://bitbucket.org/wanglab-upenn/hipFG. Docker container is available at https://hub.docker.com/r/wanglab/hipfg. Contactlswang@pennmedicine.upenn.edu Supplementary informationSupplementary data are available as BioRxiv supplemental files.