BCFTOOLS STATS

Generate summary statistics and quality control reports for VCF/BCF files

BCFTOOLS STATS

Function

bcftools stats generates detailed summary statistics for VCF/BCF files, including SNP/indel counts, Ts/Tv ratio, depth distribution, and per-sample metrics.

Input Format

  • VCF (.vcf, .vcf.gz)
  • BCF (.bcf)
  • Optional Tabix/CSI indexed files

Output Format

  • Plain-text statistics report
  • Optional Tabix index (.tbi)
  • Compatible with plot-vcfstats & MultiQC

Example Usage

bcftools stats input.vcf > stats.txt
bcftools stats -s - input.vcf.gz > stats.txt
plot-vcfstats -p plots/ stats.txt
bcftools stats -r chr1:1-1000000 input.vcf.gz > region_stats.txt

Applications

  • Variant calling quality control
  • Ts/Tv ratio analysis
  • Indel distribution checks
  • Sample-level comparisons
  • Cohort-level summarization
Important Notes:
  • Use -s - for per-sample statistics.
  • Large datasets give more reliable statistical summaries.
  • Small targeted panels may produce unstable ratios.
  • Index files improve performance for large VCFs.