filter_wsaf: Filter alleles based on within-sample allele frequencies

In mrc-ide/MIPanalyzer: Filtering and analysis of MIP data

Filter alleles based on within-sample allele frequencies

Description

Drop any allele for which the within-sample allele frequency (WSAF) is below a givin threshold. Thresholds apply in both directions, for example if wsaf_min = 0.01 then alleles with a WSAF less than 0.01 *or* greater than 0.99 will be rounded to 0 or 1, respectively. Coverage is adjusted to account for dropped reads.

Usage

filter_wsaf(x, wsaf_min = 0.01, description = "filter individual allele WSAF")

Arguments

x	object of class mipanalyzer_multiallelic.
wsaf_min	alleles with counts that make a WSAF less than this threshold are dropped.
description	brief description of the filter, to be saved in the filter history.

mrc-ide/MIPanalyzer documentation built on Jan. 17, 2024, 7:16 p.m.