VCFtools Cheatsheet

Update: 2025.6.2 Reference: VCFtools GitHub

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1. Filtering Variants

The vcftools suite allows filtering of variants based on various criteria.

Examples:

# Filter variants based on quality threshold
vcftools --vcf input.vcf --recode --recode-INFO-all --out filtered_variants --minQ 30

# Extract only specific chromosomes
vcftools --vcf input.vcf --chr chr1 --chr chr2 --recode --out extracted_chromosomes

# Remove indels from the VCF file
vcftools --vcf input.vcf --remove-indels --recode --out snps_only

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2. Summarizing Statistics

Generate various summary statistics for VCF files.

Examples:

# Calculate allele frequency
vcftools --vcf input.vcf --freq --out allele_frequency

# Calculate site quality statistics
vcftools --vcf input.vcf --site-quality --out site_quality

# Generate depth statistics
vcftools --vcf input.vcf --depth --out depth_statistics

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3. Sample Subsetting

Subset samples from a VCF file based on a predefined list.

Examples:

# Subset samples using a list of sample IDs
vcftools --vcf input.vcf --keep samples.txt --recode --out subset_samples

# Exclude specific samples
vcftools --vcf input.vcf --exclude samples_to_remove.txt --recode --out filtered_samples

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4. File Conversion

Convert VCF files into other formats for further analysis.

Examples:

# Convert a VCF file to PLINK format
vcftools --vcf input.vcf --plink --out converted_file

# Export genotype data to a tab-delimited format
vcftools --vcf input.vcf --extract-FORMAT-info GT --out genotype_data

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This cheatsheet provides concise usage examples for common VCFtools commands, making it an essential reference for bioinformatics workflows. For detailed documentation, visit the VCFtools Documentation.