Variants & FASTQ / VCF filter
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The quick conditions (minimum QUAL, minimum INFO/DP, type, PASS, regions) always keep matching sites; the expression can either keep (-i) or remove (-e) matching sites, and both apply together.
Expressions are written as in bcftools, e.g. QUAL>=30 && INFO/DP>=10, TYPE="snp", FMT/DP>20 & GT="het" (both true in the same sample), ANN~"missense" (regex on the annotation). A multi-value field (such as DP4 or AF) matches if any value matches; use DP4[2] for a single value (0-based).
Regions test whether POS falls inside (1-based, inclusive); separate several regions with commas, and give a chromosome name alone for the whole chromosome.
The result gives the filtered VCF (header kept, plus one line recording the filter) to copy or download, and a short table of kept sites; the histogram compares QUAL of kept and removed sites.
Expression semantics follow bcftools view -i/-e/-t (Danecek et al. 2021, GigaScience 10:giab008); 37 expression and region combinations were checked site by site.
Runs in your browser; uncompressed VCF files up to roughly 100 MB are recommended. A bare key that exists in both INFO and FORMAT is read as INFO here.
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