object MakeMixtureVcf
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val
AlleleFractionField: String
The format field for the allele fraction to be written to.
- val HeaderLines: Seq[VCFHeaderLine]
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val
UnknownGtFilter: String
The filter that is placed on records where the full genotype cannot be computed.
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def
genotypeOf(sample: String, ctx: VariantContext, noCallIsHomRef: Boolean): Genotype
Gets the genotype of the sample, substituting in a HomRef genotype for no-calls if required.
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def
makeWriter(output: FgBioDef.PathToVcf, in: VCFHeader, lines: Seq[VCFHeaderLine], samples: String*): VariantContextWriter
Builds a header that can be used to write a mixture VCF.
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ne(arg0: AnyRef): Boolean
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def
noCall(sampleName: String): Genotype
Makes a no-call genotype object with the provided sample name.
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