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

In 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.

ctDNAtools documentation built on March 26, 2020, 7:39 p.m.