qaVariants: QA Filtering of Variants

In lawremi/VariantTools: Tools for Exploratory Analysis of Variant Calls

QA Filtering of Variants

Description

Filters a tally GRanges through a series of simple checks for strand and read position (read position) biases.

Usage

qaVariants(x, qa.filters = VariantQAFilters(...), ...)
VariantQAFilters(fisher.strand.p.value = 1e-4, min.mdfne = 10L)

Arguments

x	A tally GRanges as output by tallyVariants.
qa.filters	The filters used for the QA process, typically constructed with VariantQAFilters, see arguments below.
...	Arguments passed to VariantQAFilters, listed below.
fisher.strand.p.value	p-value cutoff for the Fisher's Exact Test for strand bias (+/- counts, alt vs. ref). Any variants with p-values below this cutoff are discarded.
min.mdfne	Minimum allowed median distance of alt calls from their nearest end of the read.

Details

There are currently two QA filters:

• Median distance of alt calls from nearest end of the read is required to be >= min.mdfne, which defaults to 10.

• Fisher's Exact Test for strand bias, using the +/- counts, alt vs. ref. If the null is rejected, the variant is discarded.

Value

For qaVariants, a tally GRanges of the variants that pass the QA checks.

For VariantQAFilters, a FilterRules object with the QA and sanity filters.

Author(s)

Michael Lawrence and Jeremiah Degenhardt

Examples

data(vignette)
qaVariants(tallies_H1993, fisher.strand.p.value = 1e-4)

lawremi/VariantTools documentation built on March 4, 2024, 11:54 a.m.