This repo is for initial investigations into the use of imputation and phasing for low coverage sequecning data, in Anopheles gambiae, using Ag1000g and VObs data as haplotype reference panels, and the program GLIMPSE, which is from the authors of SHAPEIT and uses Richard Durbins PBWT to rapidly impute and phase SNP markers.
- Sanjay Curtis Nagi (@sanjaynagi)
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and, if available, its DOI (see above).
- Create a new github repository using this workflow as a template.
- Clone the newly created repository to your local system, into the place where you want to perform the data analysis.
Configure the workflow according to your needs via editing the files in the config/ folder. Adjust config.yaml to configure the workflow execution, and samples.tsv to specify your sample setup.
Activate the conda environment:
conda activate snakemake
Test your configuration by performing a dry-run via
snakemake --use-conda -n
Execute the workflow locally via
snakemake --use-conda --cores $N
using $N cores or run it in a cluster environment via
snakemake --use-conda --cluster qsub --jobs 100
or
snakemake --use-conda --drmaa --jobs 100
If you not only want to fix the software stack but also the underlying OS, use
snakemake --use-conda --use-singularity
in combination with any of the modes above. See the Snakemake documentation for further details.