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
bcftools stats input.vcf.gz > stats.txt
View Key Metrics
bcftools stats input.vcf.gz | grep "^SN"
Output sections:
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SN
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Summary numbers
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TSTV
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Transitions/transversions
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SiS
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Singleton stats
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AF
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Allele frequency distribution
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QUAL
-
Quality distribution
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IDD
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Indel distribution
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ST
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Substitution types
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DP
-
Depth distribution
Summary Numbers (SN)
bcftools stats input.vcf.gz | grep "^SN" | cut -f3-
Reports:
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Number of samples
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Number of records
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Number of SNPs
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Number of indels
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Number of multiallelic sites
-
Number of multiallelic SNPs
Transition/Transversion Ratio
bcftools stats input.vcf.gz | grep "^TSTV"
Expected Ti/Tv ratio:
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Whole genome: ~2.0-2.1
-
Exome: ~2.8-3.3
Per-Sample Statistics
bcftools stats -s - input.vcf.gz > per_sample.txt
Compare Two VCFs
bcftools stats input1.vcf.gz input2.vcf.gz > comparison.txt
Region-Specific Stats
bcftools stats -r chr1:1000000-2000000 input.vcf.gz > region_stats.txt
Exome Statistics
bcftools stats -R exome.bed input.vcf.gz > exome_stats.txt
Plotting Statistics
Generate Plots
bcftools stats input.vcf.gz > stats.txt plot-vcfstats -p output_dir stats.txt
Creates:
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output_dir/summary.pdf
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Individual PNG files
Comparison Plots
bcftools stats file1.vcf.gz file2.vcf.gz > comparison.txt plot-vcfstats -p comparison_dir comparison.txt
bcftools gtcheck
Check Sample Identity
bcftools gtcheck -g reference.vcf.gz query.vcf.gz
Reports concordance between samples.
Detect Sample Swaps
bcftools gtcheck -G 1 input.vcf.gz > relatedness.txt
Compares all samples pairwise.
Output Format
DC 0 sample1 sample2 0.95 1234 1200
Fields:
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DC: Data type (discordance)
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Index
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Sample 1
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Sample 2
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Discordance rate
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Sites compared
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Discordant sites
Check Against Reference Panel
bcftools gtcheck -g 1000genomes.vcf.gz unknown_sample.vcf.gz
Quick Statistics with Query
Count Variants
bcftools view -H input.vcf.gz | wc -l
Count by Type
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
bcftools view -f PASS -H input.vcf.gz | wc -l
Quality Distribution
bcftools query -f '%QUAL\n' input.vcf.gz |
awk '{sum+=$1; count++} END {print "Mean QUAL:", sum/count}'
Depth Distribution
bcftools query -f '%INFO/DP\n' input.vcf.gz |
awk '{sum+=$1; count++} END {print "Mean DP:", sum/count}'
Genotype Counts
Count heterozygous sites per sample
bcftools query -f '[%GT\t]\n' input.vcf.gz |
awk -F'\t' '{for(i=1;i<=NF;i++) if($i=="0/1" || $i=="0|1") het[i]++}
END {for(i in het) print "Sample", i, "het:", het[i]}'
Allele Frequency Spectrum
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
bcftools query -l input.vcf.gz
Count Samples
bcftools query -l input.vcf.gz | wc -l
Per-Sample Variant Counts
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
bcftools stats -s - input.vcf.gz | grep "^PSC"
cyvcf2 Statistics
Basic Counts
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
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
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
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
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
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
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
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vcf-basics - View and query VCF files
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vcf-filtering - Evaluate filter impact
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vcf-manipulation - Compare call sets
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variant-calling - Assess calling quality