@authors: Joe Marcus and Harald Ringbauer
This repo holds the snakemake pipeline and scripts used to analyze ancient DNA data from Sardinia in Marcus et al. 2020.
Either use conda, or install requeire packages with pip:
pip3 install --user scipy numpy pandas snakemake cython pysam click xlrd xlwt openpyxl XlsxWriter jupyter pyfaidx scikit-learn matplotlib seaborn scikit-allel shapely
submit-snakemake.sh # Loads conda environment with packages (if available)
submit-snakemake_noconda.sh # Loads python packages internally