VCF Analyzer
Analyze variant files with bcftools
About the VCF Variant Analyzer
The VCF Variant Analyzer runs bcftools 1.10 as WebAssembly in your browser, giving you the header inspection, summary statistics and record queries you would use on a command line, with no installation and no upload.
A VCF file is the standard exchange format for sequence variants: SNPs, indels, structural variants and, increasingly, per-sample genotypes and quality values. Before you trust a variant call set you should confirm which reference build it was called against, which contigs it contains, how it was filtered, and how many variants it actually holds. That is exactly what this tool surfaces.
Variant files frequently contain human genotypes, so this tool is built to be used without ever sending your data anywhere. Everything executes in your browser tab.
What this tool does
Inspect the VCF header
Read fileformat, reference, contig, INFO, FORMAT and FILTER definitions to confirm the reference genome and understand every field before parsing records.
Summary statistics
bcftools stats reports variant counts, transition and transversion ratios, Ts/Tv, per-contig distribution and quality breakdowns in one pass.
Field queries
Extract specific columns with the query engine, for example CHROM, POS, REF and ALT, to build a quick variant summary table.
Record-level inspection
View the raw records to check INFO annotations, FILTER status and per-sample GT, AD and DP values at a specific site.
VCF and BCF support
Accepts .vcf, .bcf and .gz compressed files, so you can analyse a file exactly as you received it.
Example commands
bcftools view -hPrint the VCF header. Always check the reference and contig lines first, since positions are meaningless without them.
bcftools statsGenerate a full statistics report including per-sample and per-contig variant counts and quality metrics.
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\n'Emit a four-column table of position, reference and alternate alleles for a quick overview of the call set.
bcftools viewStream full VCF content, including the header block, to inspect individual variant records.
Frequently asked questions
Are my VCF files uploaded anywhere?
No. bcftools is compiled to WebAssembly and runs locally in your browser. Variant data, including human genotypes, is never transmitted to or stored on a server.
What bcftools version is used?
This page uses bcftools 1.10, the stable release matching the reference samtools generation most current pipelines are built against.
What does a low Ts/Tv ratio indicate?
A transition to transversion ratio far from the expected value of about 2.0 to 3.0 for human data usually points to low-quality calls, excess sequencing error, or a call set over-enriched in rare variants. Treat it as a reason to review filtering.
What is the difference between a missing genotype and a homozygous reference call?
./. means no call was made for that sample, whereas 0/0 is a positive assertion that the sample carries the reference allele. Downstream analyses must treat these very differently.
Why do VCF positions sometimes disagree with what I see in a browser genome viewer?
Most often the VCF was called against a different genome assembly than the one loaded in the viewer, or contig names differ between them. Check the reference header line and contig naming in both.
Can I filter variants by quality or impact in this tool?
This page is oriented towards inspection and querying. For production filtering and re-calling, run bcftools or GATK in a proper workflow so that every step is recorded and reproducible.
Related tools
All processing happens locally in your browser. Nothing you upload is transmitted or stored, as described in the privacy policy.