Scripts for mapping and quality control of DEST dataset
populationInfo\: Has supplemental data from the DrosEU, DrosRTEC, and DPGP files to make a unified meta-datafile. This datafile is supplemental table 1 of Kapun et al 2021. The meta-data file includes collection information, library quality filtering, inversion frequencies, weather stations and WorldClim environmental data.
mappingPipeline\: Contains dockerized mapping pipeline. Downloads data, produces bam files, filter files, gSYNC files
add_DGN_datda\: Downloads, formats, lifts-over the Drosophila Genome Nexus data into gSYNC format
snpCalling\: SNP calling based on gSYNC files. Runs PoolSNP and SNAPE using snakemake pipeline
examples: Provides a basic script to pull allele frequencies from a GDS table and also calculates the effective coverage