Analysis scripts for: Insights about variation in meiosis from 31,228 human sperm genomes

This repository holds scripts that call crossovers, determine ploidy, and perform various other analyses for data generated via Sperm-seq. The methods from the preprint/paper ("Insights about variation in meiosis from 31,228 human sperm genomes") explain the purpose of many of the scripts, and the PDF file included in this repository (_scriptdocumentation_spermseq.pdf) provides more detailed script documentation and instructions for using these scripts. The flowchart included here (_SpermSeqDataProcessingFlowchart_scriptinfo_public.pdf) gives an example workflow for using these scripts and outside tools to process Sperm-seq data. Data generated with these methods are available in the companion repository (most recent version DOI: 10.5281/zenodo.3561081).

This updated version includes bug fixes read depth processing and aneuploidy calling scripts, updated documentation (including that the flowchart is new here), and two new scripts referenced by the flowchart.