filter_variants: Variant filtering

In seqCAT: High Throughput Sequencing Cell Authentication Toolkit

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)

seqCAT documentation built on Nov. 8, 2020, 7:36 p.m.