/// <summary> /// Step 1: Load the normal het SNVs of interest. /// </summary> protected void LoadVariants(string vcfPath) { Console.WriteLine("{0} Loading variants of interest from {1}", DateTime.Now, vcfPath); this.Variants = new List<VcfVariant>(); int overallCount = 0; int countThisChromosome = 0; using (VcfReader reader = new VcfReader(vcfPath, requireGenotypes: false)) { VcfVariant variant = new VcfVariant(); while (true) { bool result = reader.GetNextVariant(out variant); if (!result) break; overallCount++; if (variant.ReferenceName != this.Chromosome) { // Shortcut: If we've seen records for the desired chromosome, then as soon as we hit another chromosome, // we can abort: if (countThisChromosome > 0) break; continue; } countThisChromosome++; // Single-allele SNVs only: if (variant.VariantAlleles.Length != 1 || variant.VariantAlleles[0].Length != 1 || variant.ReferenceAllele.Length != 1) continue; // PF variants only: if ((variant.GenotypeColumns != null && variant.GenotypeColumns.Any()) && variant.Filters != "PASS") continue; // FILTER may not say PASS for a dbSNP VCF file if (variant.GenotypeColumns != null && variant.GenotypeColumns.Any()) // not available if we use a dbSNP VCF file { if (!variant.GenotypeColumns[0].ContainsKey("GT")) continue; // no genotype - we don't know if it's a het SNV. string genotype = variant.GenotypeColumns[0]["GT"]; if (genotype != "0/1" && genotype != "1/0") continue; // Also require they have a high enough quality score: if (variant.GenotypeColumns[0].ContainsKey("GQX")) // Note: Allow no GQX field, in case we want to use another caller (e.g. Pisces) and not crash { float GQX = float.Parse(variant.GenotypeColumns[0]["GQX"]); if (GQX < 30) continue; } } // Note: Let's NOT require the variant be in dbSNP. Maybe we didn't do annotation, either because // we chose not to or because we're on a reference without annotation available. //if (variant.Identifier == ".") continue; // Remember all the variants that pass all our tests: this.Variants.Add(variant); variant = new VcfVariant(); } } Console.WriteLine("Retained {0} variants, out of {1} records for {2}", this.Variants.Count, countThisChromosome, this.Chromosome); }