callWildtype {VariantTools} | R Documentation

## Calling Wildtype

### Description

Decides whether a position is variant, wildtype, or uncallable, according to the estimated power of the given calling filters.

### Usage

    callWildtype(reads, variants, calling.filters, pos = NULL, ...)
    minCallableCoverage(calling.filters, power = 0.80, max.coverage = 1000L)

### Arguments

`reads` | The read alignments, i.e., a path to a BAM file, or the coverage, including a `BigWigFile` object.
`variants` | The called variants, a tally `GRanges`.
`calling.filters` | Filters used to call the variants.
`pos` | A `GRanges` indicating positions to query; output is in the same order. If this is `NULL`, the entire genome is considered. This is not called `which`, because we are indicating positions, not selecting from regions.
`power` | The chance of detecting a variant if one is there.
`max.coverage` | The max coverage to be considered for the minimum (should not need to be tweaked).
`...` | Arguments to pass down to `minCallableCoverage`.

### Details

For each position (in the genome, or as specified by `pos`), the coverage is compared against the return value of `minCallableCoverage`. If the coverage is above the callable minimum, the position is called, either as a variant (if it is in `variants`) or wildtype. Otherwise, it is considered a no-call.

The `minCallableCoverage` function expects and only considers the filters returned by `VariantCallingFilters`.

### Value

A logical vector (or logical `RleList` if `pos` is `NULL`), that is `TRUE` for wildtype, `FALSE` for variant, `NA` for no-call.

### Author(s)

Michael Lawrence

### Examples

    bams <- LungCancerLines::LungCancerBamFiles()
    bam <- bams$H1993

    data(vignette)
    called.variants <- callVariants(tallies_H1993)

    pos <- c(called.variants, shift(called.variants, 3))
    wildtype <- callWildtype(bam, called.variants, VariantCallingFilters(),
                             pos = pos, power = 0.85)

[Package VariantTools version 1.28.1 Index]