call_clonet: This function is a wrapper around CLONET function

In TearsWillFall/variantCall: An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

Description

This function takes multiple parameters and perform the following analysis:

Usage

call_clonet(
  bin_path = "tools/bcftools/bcftools",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  bin_path4 = "tools/ASEQ/binaries/linux64/ASEQ",
  bin_path5 = "tools/CLONET/CLONET.R",
  vcf = "",
  bam_dir = "",
  segment_data = "",
  cn_call_data = "",
  gene_data = "",
  patient_id = "",
  ref_bins = "",
  germ_pattern = "GL",
  sample_data = "",
  min_snp_cov = 10,
  min_nsnps = 10,
  min_seg_cov = 20,
  equal_betaThr = 0.9,
  max_homo_dels = 0.01,
  del_log_thr = c(-1, -0.25),
  alpha_par = 0.9,
  clonal_thr = 0.85,
  beta_thr = 0.85,
  stages = c(1, 2, 3, 4, 5, 6),
  comp_ref_map_bias = FALSE,
  beta_decimals = 3,
  ale_imb_thr = 0.5,
  beta_method = "STM",
  adm_method = "2D",
  verbose = FALSE,
  output_dir = "",
  jobs = 1,
  threads = 3
)

Arguments

bin_path	Path to bcftools binary. Default tools/bcftools/bcftools.
bin_path2	Path to bgzip binary. Default tools/htslib/bgzip.
bin_path3	Path to tabix binary. Default tools/htslib/tabix.
bin_path4	Path to ASEQ binary. Default tools/ASEQ/binaries/linux64/ASEQ
bin_path5	Path to CLONET. Default tools/CLONET/CLONET.R
vcf	REQUIRED Path to VCF file with heterozygous SNPs.
bam_dir	REQUIRED Path to directory with BAM files.
cn_call_data	REQUIRED Path to file with formated CN call data.
gene_data	REQUIRED Path to file with gene information.
patient_id	Patient ID. Default Patient
ref_bins	REQUIRED Path to file with binned reference genome.
germ_pattern	Germline pattern. Default GL
sample_data	Path to files with sample info
min_snp_cov	Minimum tumor coverage for informative SNPs. Default 10.
min_nsnps	Minimum number of SNPs per segment. Default 10.
min_seg_cov	Minimum segment coverage. Default 20.
equal_betaThr	Minimum value of beta above which the two alleles are present in the same number. Default 0.9
max_homo_dels	Homozygous deletions threshold. Default 0.01
del_log_thr	Parameters of a valid deletion used to compute Adm.global. Default c(-1,-0.25)
alpha_par	Percentage of used deletions to compute Adm.global varibility interval. Default 0.9
clonal_thr	Clonality value threshold. Default 0.85
beta_thr	Beta value threshold. Default 0.85
stages	Analysis stages to run trough.Default c(1,2,3,4,5,6)
comp_ref_map_bias	Compute reference mapping bias and to adjust beta estimation. Default FALSE
beta_decimals	Number of beta value decimals to report. Default 3
beta_method	Method for beta estimation. Default STM. Options STM/GB
adm_method	Method for admixture estimation. Default 2D. Options 1D/2D
verbose	Enables progress messages. Default FALSE.
output_dir	Path to the output directory.
jobs	Number of Samples to analyze in parallel. Default 1
threads	Number of threads per job to use. Default 3

TearsWillFall/variantCall documentation built on Oct. 15, 2021, 8:51 p.m.