├── PopGenome_Analysis
├── README.md
├── eda_batch_effects # Exploratory
├── hardfilters_variants
├── lists
├── raw_variants
├── regions
├── scrape_pubseqs
├── wgs_pe_improved_ViVIDSmpls
├── wgs_pe_improved_global
├── wgs_qc_improved_ViVIDSmpls
├── wgs_qc_improved_global
└── wgs_se_improved_global
The PopGenome_Analysis directory contains the various analysis scripts, which follow a conventional numbering system for order in which they are to be run.
VCFs will need to be created by first downloading the publicly available sequences with the snakemake modules in scrape_pubseqs. Sequences will then need to be aligned with wgs_pe_improved* snakemake modules with respect to global and VivID samples. QC will need to be performed in the same manner. Then, variants can be called with the snakemake modules in raw_variants followed by application of filtering with the hardfilters_variants module.