callWildtype: Calling Wildtype
In VariantTools: Tools for Exploratory Analysis of Variant Calls

Description Usage Arguments Details Value Author(s) Examples

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

1 2	callWildtype(reads, variants, calling.filters, pos = NULL, ...) minCallableCoverage(calling.filters, power = 0.80, max.coverage = 1000L)

`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`.

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.

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

Michael Lawrence

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)