vivaxGEN MEA-Pipeline Documentation

The MEA-Pipeline provides set of tools and Snakemake workflow for VCF processing, population genetics and GWAS analysis.

Installation

To install, execute the following command:

"${SHELL}" <(curl -L https://raw.githubusercontent.com/vivaxgen/mea-pipeline/main/install.sh)

Examples

The following are examples on how to evoke the pipeline for different analyses.

For the all following commands, it is assumed that the initial VCF files reside in the base directory.

To filter VCF files for variant with sample missingness of 0.5, then variant with MAF (minor allele frequency) of 0.1, and then filter for samples with variant missingness of 0.5:

$ mea-pl run-vcf-query -q base-V0.5-MAF0.1-S0.5

The following command filters for biallelic SNPs before appying the above criteria:

$ mea-pl run-vcf-query -q base-split-snv-dedup-V05-MAF0.1-S0.5

The following set the minimum depth to 10 and set the het calls if the count and ratio (out of total) of the alternate allele reads is 5 and 0.1, respectively, before applying the above criteria:

$ mea-pl run-vcf-query -q base-HETd5r0.1-d10-split-snv-dedup-V0.5-MAF0.1-S0.5

Configuration

MEA-Pipeline requires a config.yaml file in the current working directory to run. A minimal configuration file, using PvP01_v2 reference genome, is shown here:

regions:
  - PvP01_01_v2
  - PvP01_02_v2
  - PvP01_03_v2
  - PvP01_04_v2
  - PvP01_05_v2
  - PvP01_06_v2
  - PvP01_07_v2
  - PvP01_08_v2
  - PvP01_09_v2
  - PvP01_10_v2
  - PvP01_11_v2
  - PvP01_12_v2
  - PvP01_13_v2
  - PvP01_14_v2

Updating the Pipeline

To update the pipeline, use the following command:

$ $VVGBIN/update-box

The above command will update the pipeline and all necessary dependencies.

User Documentation

Developer Documentation