bf2Vcf: Function to create a 'VCF' object with variant calls from an...
In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

bf2Vcf

R Documentation

Function to create a `VCF` object with variant calls from an array of Bayes factors.

This function thresholds the Bayes factors computed by the shearwater algorithm and creates a VCF object as output.

bf2Vcf(
  BF,
  counts,
  regions,
  samples = 1:nrow(counts),
  err = NULL,
  mu = NULL,
  cutoff = 0.05,
  prior = 0.5,
  mvcf = TRUE
)

`BF`	array of Bayes factors from `bbb`.
`counts`	array of counts from `loadAllData`.
`regions`	`GRanges` with the regions corresponding to counts and BF.
`samples`	vector of samples names.
`err`	Optional matrix of error rates, otherwise recomputed from counts.
`mu`	Optional matrix of relative frequencies, otherwise recomputed from counts.
`cutoff`	Cutoff for the posterior artifact probability below which a variant is considered to be true (default = 0.05)
`prior`	matrix of prior probabilities for finding a true call, typically from `makePrior`. Alternatively a single fixed number.
`mvcf`	boolean flag, if TRUE compute a large VCF with as many genotype columns as samples. Default TRUE. Otherwise use duplicate rows and only one genotype column. The sample is then provided by the info:PD field. Can be inefficient for large sample sizes.