create_background_panel_instance: Creates a background panel instance from a bam file (e.g....

In alkodsi/ctDNAtools: Analyze Circulating Tumor DNA Sequencing Data

Description

This function scans the targets regions in one bam file, and reports the number of reference, non-reference reads for each loci in addition to the non-reference (VAF) allele frequency. Loci with VAF higher than vaf_threshold are masked with NA. This function is used internally by create_background_panel

Usage

create_background_panel_instance(
  bam,
  targets,
  reference,
  vaf_threshold = 0.05,
  tag = "",
  min_base_quality = 20,
  max_depth = 1e+05,
  min_mapq = 30,
  substitution_specific = TRUE
)

Arguments

bam	A character specifying the path to bam file.
targets	The targets data frame must have the columns chr, start and end.
reference	The reference genome as BSgenome object.
vaf_threshold	Loci with the fraction of non-reference reads above this value are masked with NA.
tag	The RG tag in the bam file. Empty string defaults to using the whole bam.
min_base_quality	The minimum base quality to count a read for a loci.
max_depth	Maximum depth for the pileup
min_mapq	The minimum mapping quality to count a read for a loci
substitution_specific	logical, whether to have the loci by substitutions.

Value

A named list having depth, alt and vaf data frames. Each has the same order of loci in rows and the input sample in columns.

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