qvals2Vcf: Function to create a 'VCF' object with variant calls from an...
In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

qvals2Vcf

R Documentation

Function to create a `VCF` object with variant calls from an array of q-values.

This function thresholds the q-values computed by the shearwater algorithm and creates a VCF object as output.

qvals2Vcf(
  qvals,
  counts,
  regions,
  samples = 1:nrow(counts),
  err = NULL,
  mu = NULL,
  cutoff = 0.05,
  mvcf = TRUE
)

`qvals`	array of q-values from `betabinLRT`.
`counts`	array of counts from `loadAllData`.
`regions`	`GRanges` with the regions corresponding to counts and qvals.
`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 q-values below which a variant is considered to be true (default = 0.05)
`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.