filter_variants {seqCAT} | R Documentation

## Variant filtering

### Description

Filter variants on sequencing depth.

### Usage

    filter_variants(data, filter_depth = 10)

### Arguments

`data` | The dataframe containing the variant data to be filtered.
`filter_depth` | Threshold for variant depth (integer; default 10).

### Details

This is a function for filtering variants on sequencing depth. Variants with a depth lower than 10 are removed by default, but can be changed in the function call.

### Value

A data frame containing the filtered variants.

### Examples

    # Load test comparisons
    data(test_comparison)

    # Filter variants
    filt_1 <- filter_variants(test_comparison)
    filt_2 <- filter_variants(test_comparison, filter_depth = 20)

[Package seqCAT version 1.4.1 Index]