VCFtools.md
Update: 2025.6.2Reference: VCFtools GitHub
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
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
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
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
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.
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