bf2Vcf {deepSNV} | R Documentation

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

### Description

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

### Usage

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

### Arguments

`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.

### Value

A `VCF` object

### Note

Experimental code, subject to changes

### Author(s)

mg14

[Package deepSNV version 1.32.0 Index]