filter_variants {seqCAT}R Documentation

Variant filtering

Description

Filter variants on several criteria.

Usage

filter_variants(data, min_depth = 10, filter_vc = FALSE,
  filter_mt = FALSE, filter_ns = FALSE)

Arguments

data

The dataframe containing the variant data to be filtered.

min_depth

Threshold for variant depth (integer).

filter_vc

Filter variants not passing filtering criteria (boolean).

filter_mt

Filter mitochondrial variants (boolean).

filter_ns

Filter non-standard chromosomes (boolean).

Details

This is a function for filtering SNV profiles on several criteria: sequencing depth, variant caller-specific filtering, mitochondrial variants and variants in non-standard chromosomes. Only filters by sequencing depth by default.

Value

A data frame containing the filtered variants.

Examples

# Load test comparisons
data(test_profile_1)

# Filter variants
filtered <- filter_variants(test_profile_1, min_depth = 15)

[Package seqCAT version 1.15.1 Index]