Filter alleles based on within-sample allele frequencies

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.

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.