callTrioDeNovo: Call sites de novo mutations from family trio data
In tkonopka/RGeneticThesaurus: Analysis of thesaurus-annotated genomic variants

Description Usage Arguments

This function performs crude mutation calling based on BAF. It searches for variants in a child sample that are not present in either parent. The calculation depends on changes in AF between child and parents.

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callTrioDeNovo(baftable, cref1 = "mother", cref2 = "father",
  csample = "child", thesaurus = FALSE, foldchange = 1.2, maxref = 0.05,
  minAF = 0.15, mincov = 10, exceptcovchr1 = c(), exceptcovchr2 = c())

`baftable`	data.frame with variants and allelic frequency
`cref1,`	string, code refererring to one of the matched controls, i.e. one of the parents. The function assumes the baftable contains columns such as cref1.thesaurus.BAF, etc as output by GeneticThesaurus software
`cref2`	string, similar to cref1
`csample`	string, code referring to the child sample. The function assumes the baftable contains columns such as csample.thesaurus.BAF, etc. as output by GeneticThesaurus software.
`thesaurus`	boolean, set TRUE to use thesaurus adjusted BAF and coverage estimates
`foldchange`	numeric, required fold change in allelic frequency
`maxref`	numeric, maximal allelic frequency allowed in the reference samples
`minAF`	numeric, minimum allelic frequency required in the child sample
`mincov`	numeric, minimum coverage required in the reference samples
`exceptcovchr1`	vector of chromosome names that should be excluded from the minimum coverage requirement (e.g. set chrY for a female sample)
`exceptcovchr2`	vector, similar to exceptcovchr1