VCF Manipulation Usage Guide

VCF Manipulation Usage Guide

Overview

This guide covers merging, concatenating, sorting, and comparing VCF files.

Prerequisites

• bcftools installed (conda install -c bioconda bcftools)
• Input VCFs should be compressed (.vcf.gz) and indexed for most operations
• Index files with bcftools index input.vcf.gz

Quick Start

Tell your AI agent what you want to do:

• "Merge VCF files from different samples into a single cohort VCF"
• "Concatenate per-chromosome VCFs into a genome-wide file"
• "Compare two variant callsets and find shared and unique variants"
• "Extract specific samples from a multi-sample VCF"

Understanding Merge vs Concat

These two operations are commonly confused:

Merge Scenario

You have variants called separately for each sample:

sample1.vcf.gz  →  contains only sample1
sample2.vcf.gz  →  contains only sample2
sample3.vcf.gz  →  contains only sample3

Use bcftools merge to combine into one multi-sample VCF.

Concat Scenario

You have variants called in parallel by chromosome:

chr1.vcf.gz  →  all samples, chromosome 1
chr2.vcf.gz  →  all samples, chromosome 2
chr3.vcf.gz  →  all samples, chromosome 3

Use bcftools concat to combine into one genome-wide VCF.

Merging VCF Files

Basic Merge

bcftools merge sample1.vcf.gz sample2.vcf.gz sample3.vcf.gz -Oz -o merged.vcf.gz
bcftools index merged.vcf.gz

Merge from File List

For many samples, create a file list:

# Create list of VCF files
ls *.vcf.gz > vcf_list.txt

# Merge all
bcftools merge -l vcf_list.txt -Oz -o merged.vcf.gz

Handling Missing Data

When samples have variants at different positions:

# Default: missing genotypes shown as ./.
bcftools merge sample1.vcf.gz sample2.vcf.gz -Oz -o merged.vcf.gz

# Treat missing as homozygous reference
bcftools merge --missing-to-ref sample1.vcf.gz sample2.vcf.gz -Oz -o merged.vcf.gz

Sample Name Conflicts

If VCFs have the same sample name:

# Force merge (keeps both with modified names)
bcftools merge --force-samples file1.vcf.gz file2.vcf.gz -Oz -o merged.vcf.gz

Merge with Multi-threading

bcftools merge --threads 4 -l vcf_list.txt -Oz -o merged.vcf.gz

Concatenating VCF Files

Concatenate by Chromosome

# Files must be in order
bcftools concat chr1.vcf.gz chr2.vcf.gz chr3.vcf.gz -Oz -o genome.vcf.gz
bcftools index genome.vcf.gz

Concatenate All Chromosomes

bcftools concat chr{1..22}.vcf.gz chrX.vcf.gz chrY.vcf.gz chrM.vcf.gz -Oz -o genome.vcf.gz

From File List (Ordered)

# files.txt must list VCFs in genomic order
bcftools concat -f files.txt -Oz -o concatenated.vcf.gz

Allow Overlapping Regions

When files may contain overlapping regions:

bcftools concat -a file1.vcf.gz file2.vcf.gz -Oz -o combined.vcf.gz

Remove Duplicates While Concatenating

# Remove exact duplicate records
bcftools concat -a -d exact file1.vcf.gz file2.vcf.gz -Oz -o combined.vcf.gz

# Remove duplicate variants (same position and alleles)
bcftools concat -a -d all file1.vcf.gz file2.vcf.gz -Oz -o combined.vcf.gz

Sorting VCF Files

Basic Sort

bcftools sort input.vcf -Oz -o sorted.vcf.gz
bcftools index sorted.vcf.gz

Large File Sort

Use temporary directory and memory limit:

bcftools sort -T /scratch/tmp -m 4G input.vcf.gz -Oz -o sorted.vcf.gz

Intersecting VCF Files

Compare Two Call Sets

bcftools isec -p comparison_dir caller1.vcf.gz caller2.vcf.gz

This creates:

• comparison_dir/0000.vcf - Variants only in caller1
• comparison_dir/0001.vcf - Variants only in caller2
• comparison_dir/0002.vcf - Shared variants (from caller1)
• comparison_dir/0003.vcf - Shared variants (from caller2)

Output Compressed Files

bcftools isec -p comparison_dir -Oz caller1.vcf.gz caller2.vcf.gz

Get Only Shared Variants

# Variants present in both files
bcftools isec -n=2 -w1 caller1.vcf.gz caller2.vcf.gz -Oz -o shared.vcf.gz

Get Private Variants

# Variants only in file1 (not in file2)
bcftools isec -C caller1.vcf.gz caller2.vcf.gz -Oz -o only_in_caller1.vcf.gz

Multi-File Comparison

# Find variants present in all 3 files
bcftools isec -n=3 -w1 file1.vcf.gz file2.vcf.gz file3.vcf.gz -Oz -o in_all_three.vcf.gz

# Find variants present in at least 2 of 3 files
bcftools isec -n+2 -w1 file1.vcf.gz file2.vcf.gz file3.vcf.gz -Oz -o in_at_least_two.vcf.gz

Understanding -n Options

Subsetting VCF Files

Extract Specific Samples

bcftools view -s sample1,sample2,sample3 input.vcf.gz -Oz -o subset.vcf.gz

Exclude Specific Samples

bcftools view -s ^sample4,sample5 input.vcf.gz -Oz -o without.vcf.gz

From Sample List File

# samples.txt: one sample name per line
bcftools view -S samples.txt input.vcf.gz -Oz -o subset.vcf.gz

# Exclude samples in list
bcftools view -S ^samples.txt input.vcf.gz -Oz -o without.vcf.gz

Extract Region

bcftools view -r chr1:1000000-2000000 input.vcf.gz -Oz -o region.vcf.gz

Extract Multiple Regions

# From BED file
bcftools view -R targets.bed input.vcf.gz -Oz -o targets.vcf.gz

# Multiple regions
bcftools view -r chr1:1000-2000,chr2:3000-4000 input.vcf.gz -Oz -o regions.vcf.gz

Renaming Samples

Create Rename File

# Format: old_name<tab>new_name
cat > rename.txt << EOF
SRR123456	patient_001
SRR123457	patient_002
SRR123458	patient_003
EOF

Apply Rename

bcftools reheader -s rename.txt input.vcf.gz -o renamed.vcf.gz

Verify Rename

# Before
bcftools query -l input.vcf.gz

# After
bcftools query -l renamed.vcf.gz

Splitting VCF Files

Split by Sample

for sample in $(bcftools query -l input.vcf.gz); do
    bcftools view -s "$sample" input.vcf.gz -Oz -o "${sample}.vcf.gz"
    bcftools index "${sample}.vcf.gz"
done

Split by Chromosome

for chr in chr1 chr2 chr3 chr4 chr5; do
    bcftools view -r "$chr" input.vcf.gz -Oz -o "${chr}.vcf.gz"
    bcftools index "${chr}.vcf.gz"
done

Complete Workflow Examples

Merge Per-Sample VCFs into Cohort

# List all sample VCFs
ls samples/*.vcf.gz > sample_vcfs.txt

# Merge with missing handled as reference
bcftools merge -l sample_vcfs.txt --missing-to-ref -Oz -o cohort.vcf.gz
bcftools index cohort.vcf.gz

# Verify samples
bcftools query -l cohort.vcf.gz

Combine Parallel Chromosome Calls

# After calling variants in parallel by chromosome
for chr in chr{1..22} chrX chrY chrM; do
    bcftools index "output/${chr}.vcf.gz"
done

# Concatenate all
bcftools concat output/chr*.vcf.gz -Oz -o genome.vcf.gz
bcftools index genome.vcf.gz

Compare Caller Results

# Compare GATK vs bcftools
bcftools isec -p caller_comparison gatk.vcf.gz bcftools.vcf.gz

# Count variants in each category
echo "GATK only: $(bcftools view -H caller_comparison/0000.vcf | wc -l)"
echo "bcftools only: $(bcftools view -H caller_comparison/0001.vcf | wc -l)"
echo "Shared: $(bcftools view -H caller_comparison/0002.vcf | wc -l)"

Extract Case vs Control Samples

# samples_case.txt and samples_control.txt contain sample names

# Extract cases
bcftools view -S samples_case.txt cohort.vcf.gz -Oz -o cases.vcf.gz
bcftools index cases.vcf.gz

# Extract controls
bcftools view -S samples_control.txt cohort.vcf.gz -Oz -o controls.vcf.gz
bcftools index controls.vcf.gz

Troubleshooting

"different samples" Error

You're using concat when you should use merge, or vice versa:

• merge = same positions, different samples
• concat = same samples, different positions

"not sorted" Error

Input files must be sorted for concat:

bcftools sort input.vcf.gz -Oz -o sorted.vcf.gz

Or allow unsorted with -a:

bcftools concat -a file1.vcf.gz file2.vcf.gz -Oz -o combined.vcf.gz

"index required" Error

Many operations need indexed input:

bcftools index input.vcf.gz

"sample name conflict" Warning

Samples have the same name in different files:

# Either rename samples first
bcftools reheader -s rename.txt input.vcf.gz -o renamed.vcf.gz

# Or force merge
bcftools merge --force-samples file1.vcf.gz file2.vcf.gz -Oz -o merged.vcf.gz

Example Prompts

"Merge VCF files from different samples into a single cohort VCF"

"Concatenate per-chromosome VCFs into a genome-wide file"

"Compare two variant callsets and find shared and unique variants"

"Extract specific samples from a multi-sample VCF"

See Also

• bcftools merge documentation
• bcftools concat documentation
• bcftools isec documentation
• vcf-basics - View and query VCF files
• filtering-best-practices - Filter variants before manipulation