Genotype at a Position in My VCF
Look up the genotype at one position, or one ID, in your own VCF without uploading it.
Open the calculator → Runs in your browser. Data leaves only if you deliberately send a problem report from the interactive tool.
Example
- Position
- 20:14370 in NA00003
- Record
- REF G, ALT A, QUAL 29, FILTER PASS
Result: 20:14370: 1/1, homozygous alternate in NA00003.
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; a chromosome and position (with REF and ALT if you know them) or an ID from the ID column; a sample name if the file has more than one. The file stays in the browser tab.
- What you get
- The matching record's REF, ALT, QUAL and FILTER, and the sample's GT as written, phase, zygosity, DP, GQ and allele balance, with the assembly the file states. A position the file does not list reads "not in this file", never "reference".
What this is
Large and bgzipped files are read a piece at a time, with progress and a Stop button.
When to use it
Use this when a report or a paper names a variant and you want to see what your VCF says at that position: the genotype as written, its zygosity, depth, quality and allele balance.
How this is calculated
Citation
VCFv4.5 specification (samtools hts-specs): fixed columns, GT phasing and missing alleles, FORMAT keys, and positions sorted within each chromosome; SAMv1 section 4.1 for BGZF. Reports the genotype as the file writes it; no annotation or build conversion. Read the source ↗
A reference and educational tool. Not medical, legal, or financial advice, and not a substitute for clinician judgment.