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Product prices and availability are accurate as of the date/time indicated and are subject to change. This page lists all VCF records normalized to that variant coordinate.Important Disclaimer:We may get commissions for products or services purchased via links on our site. You can search on an unnormalized variant, and it will take you to the normalized variant’s details page. If any variants were altered during an import, a warning appears on the VCF and Sample pages, allowing you to examine the changes. We Decompose and Normalise variants using VT during import, so variants from different VCF files have a consistent representation. Thus, if both parents had reference bases, the calls would be: ProbandĪnd you can be confident that it is a denovo variant, rather than just lacking coverage in one of the parent samples.
If you merge them using GATK/ Picard using bam files - the caller will re-examine the reads over the locus, and make the genotype call. Merging just the VCFs (without supplying the bams) will give the genotypes of: Proband There’s no way to tell if a variant not being present in a single sample VCF is due to having the reference allele or no coverage. You must use bam files, to re-call the genotypes for each position. This allows you to differentiate between reference calls and no coverage - and is extremely important for Trios so that you can make correct calls about inheritance and denovo variants Multi-sample VCF files combined using bam files record the genotype for all samples at each variant position. Samples with variants type of_somatic only_ are checked for mutational signatures Multi-sample VCFs ¶
This is determined by looking at the “source” entry in the VCF header, and matching it to an entry in VCFSource object (setup by your administrator) The VCF format can vary a lot, we have tested VCFs from the following variant callers:Įach sample is assigned a “variants type” of Unknown, Germline, Mixed (single sample) or Somatic only (tumor minus normal). We only import variants, filters and genotypes (we don’t use INFO as we do our own annotations)
Variants are normalized (see below) upon import.
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