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Pre-Imputation Pipeline

Nextflow pipeline to prepare your data for Genotype Imputation

Requirements

Before running this pipeline, make sure you have the following dependencies installed:

curl -s https://get.nextflow.io | bash
  • Docker

Installation

Build docker image before run the pipeline:

docker build -t genepi/pre-imputation-qc . # don't ingore the dot here

Test the pipeline and the created docker image with test-data:

nextflow run main.nf

Usage

Create a config file (e.g. my-project.config in your project folder) and set the paths to your data:

params.project = "my-project"
params.input = "data/*/*.{map,ped}"
params.output = "output"
params.chip = "GSAMD-24v3-0-EA_20034606_A1.b37"
params.strand_file = "data/${params.chip}.strand"
params.refalt_file = "data/${params.chip}.RefAlt"

params.chunkSize= 20000000
params.minSampleCallRate = 0.5
params.minSnpCallRate = 0.9

Execute it the pipeline with you project specific configuration from your project folder:

nextflow run main.nf -c my-project.config

A html report is created in output and the vcf.gz are ready to submit them to the Michigan Imputation Server.

Parameters

Here's a table of the parameters along with their descriptions and default values:

Parameter Description Default Value Required
project Name of the project null Yes
input Directory containing input PLINK files null Yes
output Output directory for pipeline results "output/genotyped" Yes
chip Type of genotyping chip used null Yes
build Reference genome build (e.g., hg19, hg38) null Yes
strand_file Path to the strand file null Yes
refalt_file Path to the reference/alternate allele file null Yes
chunkSize Chunk size for processing data 20000000 No
minSampleCallRate Minimum sample call rate threshold 0.5 No
minSnpCallRate Minimum SNP call rate threshold 0.9 No
maf Minor allele frequency threshold 0 No
hwe Hardy-Weinberg equilibrium p-value threshold 1E-6 No
cleanSampleIds Clean sample IDs (true/false) false No
excludeSamples File containing samples to exclude null No
useDoubleId Use double IDs for samples (true/false) true No

These parameters allow customization of the pipeline's behavior and thresholds for various data processing steps. You can adjust these values as needed to fit your specific project requirements.

Workflow

  1. Clean Sample IDs: (Optional) Clean sample IDs in input files if specified.

  2. Exclude Samples: (Optional) Exclude specified samples from the analysis.

  3. Filter and Fix Strand Flips: Filter and fix strand flips using provided strand and ref/alt allele files.

  4. Merge VCF Files: Merge filtered VCF files.

  5. Filter Merged VCF: Further filter the merged VCF file.

  6. Create Final PLINK: Generate the final PLINK files.

  7. Split Into Chromosomes: Split the final PLINK files into separate chromosomes.

  8. Create Report: Generate a report summarizing the pipeline's execution.

Outputs

  • Processed PLINK files for each chromosome.
  • Various reports and statistics files.

Contact

Lukas Forer (@lukfor), Institute of Genetic Epidemiology, Medical University of Innsbruck

License

This pipeline is distributed under the MIT License.