filter_variants {vivaldi}

filter_variants

Description

Filters single-nucleotide variants using a coverage and frequency cutoff

Usage

filter_variants(df, coverage_cutoff = 200, frequency_cutoff = 0.03)

Arguments

df

A rearranged VCF dataframe (rearranged using the arrange_data function)

coverage_cutoff

The coverage cutoff for calling a SNV (default: 200x)

frequency_cutoff

Frequency cutoff for calling a SNV (default: 3%)

Value

A filtered VCF dataframe

Examples

df <- data.frame(CHROM = c("A", "B", "C"),
                POS = c(234, 240, 255),
                ALT_FREQ = c(0.016, 0.049, 0.031),
                gt_DP = c(716, 600, 187)
)

df

# Default: filter by 3% frequency threshold and 200 coverage cutoff
filter_variants(df)

# Example 1: A 1% allele frequency threshold and 200 coverage cutoff
filter_variants(df, coverage_cutoff = 200, frequency_cutoff = 0.01)

# Example 2: A 2% allele frequency threshold and 100 coverage cutoff
filter_variants(df, coverage_cutoff = 100, frequency_cutoff = 0.02)