smsk_popoolation: A Snakemake pipeline for population genomics

1. Description

This is a repo that contains installers and snakemake scripts to execute the pipelines described by Kofler et al. in popoolation 1 and 2:

• Mapping with bwa-mem2

• BAM wrangling and SNP calling with samtools and picard

• Population measures with popoolation. Computation of expected heterozygosity h_p with a python script.

• Pairwise comparisons between populations with popoolation2

2. First steps

1. Install (ana|mini)conda

2. Clone and install the software

   git clone https://github.com/jlanga/smsk_popoolation.git smsk_popoolation
   cd smsk_popoolation
   snakemake --use-conda --create-envs-only

3. Run the test dataset:

   snakemake --use-conda -c 8

4. Modify the following files:

   • config/features.yaml: the path to the genome reference, and the names of every chromosome to be processed.

   • config/samples.tsv: paths and library information of each of the samples.

   • config/params.yml: execution parameters of different tools.

5. Execute the pipeline:

   snakemake --use-conda -j

Representation of the pipeline

Bibliography

• A Quick Guide to Organizing Computational Biology Projects

• Snakemake—a scalable bioinformatics workflow engine

• popoolation

• popoolation2

• samtools