Genotype Processing Scripts

This repository provides Bash and R scripts to efficiently process and analyze genotype files.

Features

1. Genotype File Processing (SNP_in_cols.sh and edit_genotypes.sh)

• Work with genotype files, including chromosome.data and imputed_genotypefiles.

2. File Comparison (edit_genotypes.sh)

• Compare genotype files to:
  • Identify SNP removals.
  • Detect updates in genotype files.

3. Quality Control (QC-SNP.R)

Perform quality control checks on genotype data, including:

• Call Rate: Ensure sufficient SNP call coverage.
• Call Frequency: Verify the frequency of SNP calls.
• Minor Allele Frequency (MAF): Exclude SNPs with low-frequency alleles.

4. Kernel Computation

• Compute:
  • Linear kernels.
  • Gaussian kernels.

Requirements

Software

• Bash: For processing pipeline scripts.
• R: Version 4.0+ recommended.