Why Allele Balance Matters
Allele balance shows how much read support belongs to an alternate allele. It is often checked in VCF review. A balanced heterozygous call usually has similar reference and alternate read support. A very low balance can suggest noise, mapping bias, strand issues, sample mixture, or a weak call. The calculator helps you inspect those values before deeper review.
Reading VCF Depth Fields
VCF files often store read counts in the AD field. The first AD value usually represents reference reads. Later values represent alternate alleles. For a biallelic site, AD=18,12 means 18 reference reads and 12 alternate reads. The alternate allele balance is 12 divided by 30. That gives 0.4000, or 40.00 percent.
Flexible Input Options
This tool also accepts FORMAT and SAMPLE strings. It can read AD, DP, GT, and GQ when those keys exist. This is useful when copying one sample column from a VCF line. You may also enter read counts manually. Manual fields are helpful when the source uses a custom tag.
Review Thresholds
Use the minimum depth filter to catch thin evidence. Use the balance range to set your review limits. A common heterozygous review range is 0.30 to 0.70. That range is not universal. Tumor samples, pooled samples, mosaic sites, copy number changes, and contamination can shift expected balance. Always compare results with your assay design and quality rules.
Understanding the Report
The report shows alternate balance, reference balance, variant allele fraction, total depth, selected allele support, and status. It also explains which input source was used. This reduces confusion when several VCF fields are present.
Advanced Review Notes
Advanced review needs context. A homozygous alternate genotype should trend toward high alternate support. A reference genotype should trend toward low alternate support. Multi allelic records need the correct alternate index. Low depth can make any ratio unstable. High depth can still be biased by alignment or chemistry effects.
Exporting Results
Exports are useful for batch notes. CSV files work well in spreadsheets. PDF reports are useful for summaries, reviews, and internal records. The result should not replace expert variant interpretation. It is a quick numeric check for read support. Confirm flagged variants with the full VCF, alignment view, filters, and laboratory standards. Save the chosen thresholds with each export. This makes repeat review easier later too.