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 1.12.0 Index]