Snakemake workflow:

This Snakemake workflow is to be used for phasing imputed genotype data from the Norwegian Mother, Father and Child Cohort study, which includes parent-offspring duos and trios, as well as non-related individuals.

Authors

• Pol Sole-Navais (@psnavais) - pol.sole.navais@gu.se

Dependencies

• Global environment to run the Snakemake pipeline (not all required):

• python=3.8.10
• numpy=1.23.3
• pandas=1.5.0
• scipy=1.9.1
• bedtools=2.30.0
• bcftools=1.15.1
• mamba=0.25.0

• Other dependencies can be found under the workflow/envs/ folder (see below).

Structure

All scripts needed to run this pipeline are contained in the workflow folder.

• Snakefile: main Snakefile, calls other snakefiles and lists files to be collected
• envs: contains the .yml environment files to run this pipeline
• rules: contains the rules for each of the steps in the pipeline in different Snakefiles (.smk)
• scripts: contains R and python scripts used by the pipeline
• report: not used
• schemas: not used

Usage

Call snakemake from the main folder - it will automatically detect that the main Snakefile is in the workflow folder. Beware that the pipeline is computationally intensive (both memory and threads used) because it is run on imputed genetic data.