Variants & FASTQ / VCF comparison
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By default a variant is shared only if CHROM, POS, REF and ALT are all identical (multiallelic sites compare their ALT sets as a whole), as in the default bcftools isec rule; “position only” also counts different alleles at the same position as shared.
The Venn diagram shows shared and private sites and the bar chart splits them by variant type; Jaccard = shared / union.
Genotypes are paired by sample name when names match (otherwise by column order): concordance = genotypes with identical alleles / genotypes non-missing on both sides; non-reference discordance considers only genotypes that are non-reference on at least one side.
Make sure both VCFs use the same reference genome and chromosome names. Indels written differently (e.g. left-aligned or not) count as different variants, so normalise them first if needed.
Site matching follows bcftools isec (Danecek et al. 2021, GigaScience 10:giab008); the shared and private site lists were checked one by one on real and simulated data.
Runs in your browser; up to roughly 100 MB in total for the two files is recommended.
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