Variants & FASTQ / VCF statistics
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The summary shows the number of records, SNPs and indels and the transition/transversion ratio (Ts/Tv). Germline whole-genome SNPs usually give Ts/Tv of about 2.0–2.1 and exome regions about 2.8–3.0; a much lower value often points to many false positives.
Types follow bcftools stats: a site with several ALT alleles counts once as a SNP if any allele is a SNP and once as an indel if any allele is an indel; substitution types use SNP alleles only.
Per-sample statistics split genotypes into hom-ref, hom-alt, het, haploid (e.g. bacteria) and missing; mean depth uses FORMAT/DP (DP = 0 is left out), matching the bcftools PSC definitions.
Use the QUAL and INFO/DP histograms to choose filtering thresholds, then apply them in the VCF filter tool.
Definitions follow bcftools stats (Danecek et al. 2021, GigaScience 10:giab008) and were checked item by item on the example and on simulated multi-sample data; format per the VCFv4.2 specification.
Runs in your browser; uncompressed VCF files up to roughly 100 MB are recommended.
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