call_aasuite: Wrapper around assuite

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Wrapper around assuite

Description

Wrapper around AmpliconArchitectSuite

Usage

call_aasuite(
  sif_aa = build_default_sif_list()$sif_aa,
  bin_aasuite = build_default_tool_binary_list()$bin_aasuite,
  cns = NULL,
  bam = NULL,
  cn_gain = 4.5,
  cnsize_min = 50000,
  downsample = 10,
  run_AA = TRUE,
  run_AC = TRUE,
  AA_runmode = "FULL",
  AA_extendmode = "EXPLORE",
  AA_insert_sdevs = 3,
  ...
)

Arguments

sif_aa	Path to AmpliconArchitect sif
bin_aasuite	Path to AmpliconArchitect-suite
cns	Path to BED file with seeds or segmentation
bam	Path to BAM file.
cn_gain	Minimum cn_gain
cnsize_min	Minimum cnsize
downsample	Downsample BAM file
run_AA	Run AmpliconArchitect
run_AC	Run AmpliconClassifier
AA_runmode	AmpliconArchitect runmode
AA_extendmode	AmpliconArchitect extendedmode
AA_insert_sdevs	AmpliconArchitect inster sdevs

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.