VCF Summary: Variant Counts, Ti/Tv and Zygosity
Count what is in your own VCF without uploading it: records, PASS calls, variant types, transitions and transversions, and one sample's zygosity.
Open the calculator → Runs in your browser. Data leaves only if you deliberately send a problem report from the interactive tool.
Example
- Records
- 5, 4 PASS
- NA00003
- 0 heterozygous, 3 homozygous alternate
Result: 5 records, 4 PASS; Ti/Tv 1.00; NA00003 het/hom-alt 0.00.
Answer the questions this way to reach that result. Your own answers give your own.
Inputs and output
- What you enter
A .vcf, .vcf.gz or .vcf.bgz file and, if it has more than one sample, the sample to count. The file stays in the browser tab.
- What you get
- Record, PASS, reference-only and multiallelic counts; SNV, insertion, deletion and other ALT alleles; transitions, transversions and Ti/Tv; the sample's heterozygous, homozygous-alternate, reference and missing calls and het/hom-alt; counts per chromosome; the bytes read. No expected range is printed.
What this is
Large and bgzipped files are read a piece at a time.
When to use it
Use this to check a VCF before using it: whether it is the file you think it is, how many calls passed the caller's filters, and whether its Ti/Tv and het/hom-alt ratios look like the kind of data it should be.
How this is calculated
Citation
VCFv4.5 specification (samtools hts-specs): records, FILTER, REF and ALT alleles and per-sample GT. Transitions are A<->G and C<->T substitutions. No expected range is given: Ti/Tv and het/hom-alt depend on capture, caller and ancestry. Read the source ↗
A reference and educational tool. Not medical, legal, or financial advice, and not a substitute for clinician judgment.