BCFtools

BCFtools is the standard toolkit for manipulating VCF and BCF variant files. Liatir uses the stats subcommand to compute summary statistics from a variant callset.

Details

Property	Value
Type	Native tool
Binary	bcftools
Subcommand	stats

Installation

BCFtools must be installed and available in your system PATH.

macOS (Homebrew)

brew install bcftools

Ubuntu/Debian

sudo apt install bcftools

conda

conda install -c bioconda bcftools

Accepted inputs

Extension	Description
.vcf	Uncompressed VCF
.vcf.gz	Bgzip-compressed VCF (requires .tbi index for random access; not needed for stats)
.bcf	Binary call format
.bcf.gz	Compressed BCF

VCF vs BCF

BCF is the binary equivalent of VCF, roughly analogous to BAM vs SAM. BCF files are faster to parse and smaller on disk but require BCFtools or htslib to inspect. For bcftools stats, either format works identically.

Running BCFtools stats

1. Navigate to Tools → BCFtools.
2. Select a VCF or BCF file from your Data library.
3. Click Run.

The run executes bcftools stats <path> and parses the structured output sections.

Output metrics

Summary counts

Metric	Description
Total records	All variant records in the file
SNPs	Single-nucleotide polymorphisms (REF and ALT are both single bases)
Indels	Insertions and deletions
MNPs	Multi-nucleotide polymorphisms
Other	Complex variants not in the above categories
Multiallelic sites	Sites with more than one ALT allele

Transitions and transversions

Transitions (Ts) are substitutions between chemically similar bases: A↔G (purines) and C↔T (pyrimidines). Transversions (Tv) are substitutions between dissimilar bases: A↔C, A↔T, G↔C, G↔T.

Biological mutation rates favour transitions over transversions, so the Ts/Tv ratio is a standard quality indicator:

Ts/Tv ratio	Context
≥ 2.8	Expected for whole-exome sequencing
~2.0–2.1	Expected for whole-genome sequencing
≥ 1.8	Generally acceptable for WGS
< 1.8	May indicate false positives or low-quality calls

Low Ts/Tv

A Ts/Tv below 1.8 often signals a high false-positive rate in the callset. This typically appears when variant caller quality thresholds are too permissive, or when the sample has very low coverage. Consider tightening QUAL or FILTER thresholds before downstream analysis.

Per-sample statistics (multi-sample VCF)

When the input VCF contains multiple samples, bcftools stats reports per-sample counts:

Metric	Description
Homozygous ref	Sites where the sample is homozygous reference
Homozygous alt	Sites where the sample is homozygous alternate
Heterozygous	Sites where the sample is heterozygous
Ts/Tv (per sample)	Per-sample transition-to-transversion ratio

High variability in per-sample Ts/Tv within the same cohort may indicate technical differences between samples (e.g., different sequencing batches or coverage levels).