postFilterVariants {VariantTools} | R Documentation

## Post-filtering of Variants

### Description

Applies filters to a set of called variants. The only current filter is a cutoff on the weighted neighbor count of each variant. This filtering is performed automatically by `callVariants`, so these functions are for when more control is desired.

### Usage

    postFilterVariants(x, post.filters = VariantPostFilters(...), ...)
    VariantPostFilters(max.nbor.count = 0.1, whitelist = NULL)

### Arguments

`x` | A tally `GRanges` containing called variants, as output by `callVariants`.
`post.filters` | The filters applied to the called variants.
`...` | Arguments passed to `VariantPostFilters`, listed below.
`max.nbor.count` | Maximum allowed number of neighbors (weighted by distance)
`whitelist` | Positions to ignore; these will always pass the filter, and are excluded from the neighbor counting.

### Details

The neighbor count is calculated within a 100bp window centered on the variant. Each neighbor is weighted by the inverse square root of the distance to the neighbor. This was motivated by fitting logistic regression models including a term the count (usually 0, 1, 2) at each distance. The inverse square root function best matched the trend in the coefficients.

### Value

For `postFilterVariants`, a tally `GRanges` of the variants that pass the filters.

For `VariantPostFilters`, a `FilterRules` object with the filters.

### Author(s)

Michael Lawrence and Jeremiah Degenhardt

### Examples

    bams <- LungCancerLines::LungCancerBamFiles()
    ## post-filters are not enabled by default during calling
    data(vignette)
    called.variants <- callVariants(tallies_H1993)
    ## but can be applied at a later time...
    postFilterVariants(called.variants, max.nbor.count = 0.15)

    # or enable during calling
    called.variants <- callVariants(tallies_H1993,
                                    post.filters = VariantPostFilters())

[Package VariantTools version 1.35.0 Index]