RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data

Abstract

SummaryHere, we introduce RatesTools, an automated pipeline to infer de novo mutation rates from parent-offspring trio data of diploid organisms. By providing a reference genome and high-coverage, whole-genome resequencing data of a minimum of three individuals (sire, dam, offspring), RatesTools provides a list of candidate de novo mutations and calculates a putative mutation rate. RatesTools uses several quality filtering steps, such as discarding sites with low mappability and highly repetitive regions, as well as sites with low genotype and mapping qualities to find potential de novo mutations. In addition, RatesTools implements several optional filters based on post hoc assumptions of the heterozygosity and mutation rate of the organism. Filters are highly customizable to user specifications in order to maximize utility across a wide-range of applications. AvailabilityRatesTools is freely available at https://github.com/campanam/RatesTools under a Creative Commons Zero (CC0) license. The pipeline is implemented in Nextflow (Di Tommaso et al. 2017), Ruby (http://www.ruby-lang.org), Bash (https://www.gnu.org/software/bash/), and R (R Core Team 2020) with reliance upon several other freely available tools. RatesTools is compatible with macOS and Linux operating systems. Supplementary InformationWe document RatesTools performance using published datasets in the online Supplementary information.