build_default_hatchet_config: Build default references

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

Build default references

Description

Build default references

Usage

build_default_hatchet_config(
  configs = list(download_panel = list(run = FALSE, config = list(ref_panel =
    "1000GP_Phase3", refpaneldir =
    "/lustre/scratch/scratch/regmova/TRIALS/HATCHET/reference/panel")), genotype_snps =
    list(run = TRUE, config = list(mincov = 8, maxcov = 300, reference_version = "hg19",
    chr_notation = "False")), count_alleles = list(run = TRUE, config = list(mincov = 8,
    maxcov = 300)), count_reads = list(run = TRUE, config = list()), phase_snps =
    list(run = TRUE, config = list(refpaneldir =
    "/lustre/scratch/scratch/regmova/TRIALS/HATCHET/reference/panel")), 
    
    combine_counts = list(run = TRUE, config = list(msr = 3000, mtr = 5000)),
    cluster_bins = list(run = TRUE, config = list(diploidbaf = 0.1, minK = 2, maxK = 30,
    tau = 1e-06, transmat = "\"diag\"", decoding = "\"map\"", covar = "\"diag\"",
    restarts = 10)), loc_clust = list(run = TRUE, config = list()), plot_bins = list(run
    = TRUE, config = list()), compute_cn = list(run = TRUE, config = list(solver = "cpp",
    clones = "2,8", ghostprop = 0.3, tolerancerdr = 0.08, tolerancebaf = 0.04, seeds =
    400, minprop = 0.03)), 
     plot_cn = list(run = TRUE, config = list()))
)

Arguments

configs

List with reference files

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