VCF Statistics

Generate statistics and quality metrics using bcftools.

Statistics Tools

Command	Purpose
`bcftools stats`	Comprehensive variant statistics
`bcftools gtcheck`	Sample concordance and relatedness
`bcftools query`	Custom summaries

bcftools stats

Basic Statistics

bash

bcftools stats input.vcf.gz > stats.txt

View Key Metrics

bash

bcftools stats input.vcf.gz | grep "^SN"

Output sections:

SN - Summary numbers
TSTV - Transitions/transversions
SiS - Singleton stats
AF - Allele frequency distribution
QUAL - Quality distribution
IDD - Indel distribution
ST - Substitution types
DP - Depth distribution

Summary Numbers (SN)

bash

bcftools stats input.vcf.gz | grep "^SN" | cut -f3-

Reports:

Number of samples
Number of records
Number of SNPs
Number of indels
Number of multiallelic sites
Number of multiallelic SNPs

Transition/Transversion Ratio

bash

bcftools stats input.vcf.gz | grep "^TSTV"

Expected Ti/Tv ratio:

Whole genome: ~2.0-2.1
Exome: ~2.8-3.3

Per-Sample Statistics

bash

bcftools stats -s - input.vcf.gz > per_sample.txt

Compare Two VCFs

bash

bcftools stats input1.vcf.gz input2.vcf.gz > comparison.txt

Region-Specific Stats

bash

bcftools stats -r chr1:1000000-2000000 input.vcf.gz > region_stats.txt

Exome Statistics

bash

bcftools stats -R exome.bed input.vcf.gz > exome_stats.txt

Plotting Statistics

Generate Plots

bash

bcftools stats input.vcf.gz > stats.txt
plot-vcfstats -p output_dir stats.txt

Creates:

output_dir/summary.pdf
Individual PNG files

Comparison Plots

bash

bcftools stats file1.vcf.gz file2.vcf.gz > comparison.txt
plot-vcfstats -p comparison_dir comparison.txt

bcftools gtcheck

Check Sample Identity

bash

bcftools gtcheck -g reference.vcf.gz query.vcf.gz

Reports concordance between samples.

Detect Sample Swaps

bash

bcftools gtcheck -G 1 input.vcf.gz > relatedness.txt

Compares all samples pairwise.

Output Format

DC  0  sample1  sample2  0.95  1234  1200

Fields:

DC: Data type (discordance)
Index
Sample 1
Sample 2
Discordance rate
Sites compared
Discordant sites

Check Against Reference Panel

bash

bcftools gtcheck -g 1000genomes.vcf.gz unknown_sample.vcf.gz

Quick Statistics with Query

Count Variants

bash

bcftools view -H input.vcf.gz | wc -l

Count by Type

bash

# SNPs
bcftools view -v snps -H input.vcf.gz | wc -l

# Indels
bcftools view -v indels -H input.vcf.gz | wc -l

Count PASS Variants

bash

bcftools view -f PASS -H input.vcf.gz | wc -l

Quality Distribution

bash

bcftools query -f '%QUAL\n' input.vcf.gz | \
    awk '{sum+=$1; count++} END {print "Mean QUAL:", sum/count}'

Depth Distribution

bash

bcftools query -f '%INFO/DP\n' input.vcf.gz | \
    awk '{sum+=$1; count++} END {print "Mean DP:", sum/count}'

Genotype Counts

bash

# Count heterozygous sites per sample
bcftools query -f '[%GT\t]\n' input.vcf.gz | \
    awk -F'\t' '{for(i=1;i<=NF;i++) if($i=="0/1" || $i=="0|1") het[i]++}
        END {for(i in het) print "Sample", i, "het:", het[i]}'

Allele Frequency Spectrum

bash

bcftools query -f '%INFO/AF\n' input.vcf.gz | \
    awk '{
        if($1<0.01) rare++
        else if($1<0.05) low++
        else if($1<0.5) common++
        else freq++
    } END {
        print "Rare (<1%):", rare
        print "Low (1-5%):", low
        print "Common (5-50%):", common
        print "Frequent (>50%):", freq
    }'

Sample Statistics

List Samples

bash

bcftools query -l input.vcf.gz

Count Samples

bash

bcftools query -l input.vcf.gz | wc -l

Per-Sample Variant Counts

bash

for sample in $(bcftools query -l input.vcf.gz); do
    count=$(bcftools view -s "$sample" -H input.vcf.gz | \
        bcftools view -c 1 -H | wc -l)
    echo "$sample: $count"
done

Missing Genotypes per Sample

bash

bcftools stats -s - input.vcf.gz | grep "^PSC"

cyvcf2 Statistics

Basic Counts

python

from cyvcf2 import VCF

stats = {'snps': 0, 'indels': 0, 'other': 0}

for variant in VCF('input.vcf.gz'):
    if variant.is_snp:
        stats['snps'] += 1
    elif variant.is_indel:
        stats['indels'] += 1
    else:
        stats['other'] += 1

print(f'SNPs: {stats["snps"]}')
print(f'Indels: {stats["indels"]}')
print(f'Other: {stats["other"]}')

Quality Statistics

python

from cyvcf2 import VCF
import numpy as np

quals = []
for variant in VCF('input.vcf.gz'):
    if variant.QUAL:
        quals.append(variant.QUAL)

quals = np.array(quals)
print(f'Mean QUAL: {np.mean(quals):.1f}')
print(f'Median QUAL: {np.median(quals):.1f}')
print(f'Min QUAL: {np.min(quals):.1f}')
print(f'Max QUAL: {np.max(quals):.1f}')

Genotype Distribution

python

from cyvcf2 import VCF

vcf = VCF('input.vcf.gz')
samples = vcf.samples

hom_ref = [0] * len(samples)
het = [0] * len(samples)
hom_alt = [0] * len(samples)
missing = [0] * len(samples)

for variant in vcf:
    for i, gt in enumerate(variant.gt_types):
        if gt == 0:
            hom_ref[i] += 1
        elif gt == 1:
            het[i] += 1
        elif gt == 3:
            hom_alt[i] += 1
        else:
            missing[i] += 1

for i, sample in enumerate(samples):
    print(f'{sample}: HOM_REF={hom_ref[i]}, HET={het[i]}, HOM_ALT={hom_alt[i]}, MISS={missing[i]}')

Transition/Transversion Calculation

python

from cyvcf2 import VCF

transitions = 0
transversions = 0

ti_pairs = {('A', 'G'), ('G', 'A'), ('C', 'T'), ('T', 'C')}

for variant in VCF('input.vcf.gz'):
    if not variant.is_snp:
        continue
    ref = variant.REF
    alt = variant.ALT[0]
    if (ref, alt) in ti_pairs:
        transitions += 1
    else:
        transversions += 1

ratio = transitions / transversions if transversions > 0 else 0
print(f'Transitions: {transitions}')
print(f'Transversions: {transversions}')
print(f'Ti/Tv ratio: {ratio:.2f}')

Common Workflows

Quality Control Report

bash

# Generate stats
bcftools stats input.vcf.gz > stats.txt

# Extract key metrics
echo "=== VCF Summary ==="
grep "^SN" stats.txt | cut -f3-

echo ""
echo "=== Ti/Tv Ratio ==="
grep "^TSTV" stats.txt | cut -f5

# Generate plots
plot-vcfstats -p qc_plots stats.txt

Compare Before/After Filtering

bash

bcftools stats raw.vcf.gz filtered.vcf.gz > comparison.txt

echo "=== Before Filtering ==="
grep "^SN.*raw" comparison.txt | cut -f3-

echo ""
echo "=== After Filtering ==="
grep "^SN.*filtered" comparison.txt | cut -f3-

Sample Relatedness Check

bash

bcftools gtcheck -G 1 cohort.vcf.gz > relatedness.txt
cat relatedness.txt

Quick Reference

Task	Command
Full stats	`bcftools stats input.vcf.gz`
Summary only	`bcftools stats input.vcf.gz \| grep "^SN"`
Ti/Tv ratio	`bcftools stats input.vcf.gz \| grep "^TSTV"`
Per-sample	`bcftools stats -s - input.vcf.gz`
Compare VCFs	`bcftools stats file1.vcf.gz file2.vcf.gz`
Sample check	`bcftools gtcheck -G 1 input.vcf.gz`
Plot stats	`plot-vcfstats -p dir stats.txt`

Common Errors

Error	Cause	Solution
`No data`	Empty VCF	Check if VCF has variants
`plot-vcfstats not found`	Not installed	Install with bcftools
`Cannot open`	Invalid VCF	Check file format

Related Skills

vcf-basics - View and query VCF files
vcf-filtering - Evaluate filter impact
vcf-manipulation - Compare call sets
variant-calling - Assess calling quality

Search AI Tools

Install this agent skill to your Project

SKILL.md

VCF Statistics

Statistics Tools

bcftools stats

Basic Statistics

View Key Metrics

Summary Numbers (SN)

Transition/Transversion Ratio

Per-Sample Statistics

Compare Two VCFs

Region-Specific Stats

Exome Statistics

Plotting Statistics

Generate Plots

Comparison Plots

bcftools gtcheck

Check Sample Identity

Detect Sample Swaps

Output Format

Check Against Reference Panel

Quick Statistics with Query

Count Variants

Count by Type

Count PASS Variants

Quality Distribution

Depth Distribution

Genotype Counts

Allele Frequency Spectrum

Sample Statistics

List Samples

Count Samples

Per-Sample Variant Counts

Missing Genotypes per Sample

cyvcf2 Statistics

Basic Counts

Quality Statistics

Genotype Distribution

Transition/Transversion Calculation

Common Workflows

Quality Control Report

Compare Before/After Filtering

Sample Relatedness Check

Quick Reference

Common Errors

Related Skills