Quality Control Pipeline

Containerized VCF Quality Control Pipeline using PLINK and VCFtools

Overview

This containerized QC pipeline performs comprehensive quality control analysis on VCF files including relatedness analysis, gender checking, IBD analysis, and homozygosity detection.

Building the Docker Image

docker build -t quality-control .

Running the Container

Mount current directory

docker run -v $(pwd):/data quality-control QC --input_vcf /data/input.vcf.gz

Mount separate input and output directories

docker run \
  -v /home/user/vcf_files:/input:ro \
  -v /home/user/qc_results:/output \
  quality-control QC \
  --input_vcf /input/sample.vcf.gz \
  --output_directory /output \
  --vcf_prefix SampleBatch

Script Options

The QC script (Scaffold_QC.sh) accepts the following parameters:

Flag	Required	Default	Description
--input_vcf	Yes	-	Path to input VCF file (must be gzipped)
--output_directory	No	.	Output directory for results
--vcf_prefix	No	MyBatchPrefix	Prefix for output files

Examples

Minimal usage

QC --input_vcf /data/samples.vcf.gz

Full parameter specification

QC --input_vcf /data/samples.vcf.gz --output_directory /results --vcf_prefix PopulationStudy

Output Files

The pipeline generates multiple analysis files:

• Relatedness: .relatedness and .relatedness2 files
• Gender Check: .sex and .sex2 files
• IBD Analysis: .IBD.genome file
• Heterozygosity: .HET.het file
• Inbreeding Coefficient: .IBC.ibc file
• Homozygosity: .HOM.hom files
• Cleaned VCF: .C.VCF.vcf.gz with quality filters applied

Dependencies

The container includes:

• PLINK (v1.90b6.21)
• VCFtools (v0.1.16)
• HTSlib/SAMtools/BCFtools (v1.22)

Requirements

• Input VCF file must be bgzip compressed (.vcf.gz)
• Sufficient disk space for intermediate and output files
• Docker with appropriate permissions for volume mounts