filter_variants: Variant filtering

Description Usage Arguments Details Value Examples

View source: R/filter_variants.R

Description

Filter variants on several criteria.

Usage

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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

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# 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.