filter_mutations: Filters a set of mutations

In alkodsi/ctDNAtools: Analyze Circulating Tumor DNA Sequencing Data

Description

This function Filters a set of mutations given the input black list or the prevalence of their mismatches in a set of bam files. Mutations that have more than min_alt_reads in more than min_samples will be removed when no black list is given.

Usage

filter_mutations(
  mutations,
  bams = NULL,
  black_list = NULL,
  tags = rep("", length(bams)),
  min_alt_reads = 2,
  min_samples = 2,
  min_base_quality = 20,
  max_depth = 1e+05,
  min_mapq = 30,
  substitution_specific = TRUE
)

Arguments

mutations	A data frame with the reporter mutations. Should have the columns CHROM, POS, REF, ALT.
bams	a vector of paths to bam files
black_list	a character vector of genomic loci of format chr_pos to filter. If not given, the bams will be scanned for mismatches in the mutations loci and the specified thresholds will be applied for filtering.
tags	a vector of the RG tags if the bam has more than one sample
min_alt_reads	the threshold of read counts showing alternative allele for a sample to be counted
min_samples	the threshold of number of samples above which the mutations is filtered
min_base_quality	minimum base quality for a read to be counted
max_depth	maximum depth above which sampling will happen
min_mapq	the minimum mapping quality for a read to be counted
substitution_specific	logical, whether to have the loci of black_list by substitutions.

Details

Filter a set of mutations using one of two options:

1.

By providing a black list (recommended), which includes a vector of genomic loci chr_pos when substitution_specific is false, or chr_pos_ref_alt when substitutions_specific is true. In this mode, all mutations reported in the black list are simply removed.

2.

By providing a set of bam files. The function will run a similar functionality to create_background_panel and filter mutations based on the min_alt_reads and min_samples criteria.

This function is called internally in test_ctDNA so you likely won't need to use it yourself.

Value

a named list contains:

• ref: vector of read counts of the reference alleles

• alt: vector of read counts of the alternative allele

See Also

create_black_list test_ctDNA create_background_panel

Examples

data("mutations", package = "ctDNAtools")
filter_mutations(mutations, black_list = "chr14_106327474_C_G")

alkodsi/ctDNAtools documentation built on Feb. 22, 2022, 9:40 a.m.