inst/example/battenberg_snp6.R

In Wedge-lab/battenberg: Battenberg subclonal copy number caller

library(Battenberg)
library(optparse)

option_list = list(
  make_option(c("-a", "--analysis_type"), type="character", default="paired", help="Type of analysis to run: paired, cell_line, germline", metavar="character"),
  make_option(c("-s", "--samplename"), type="character", default=NULL, help="Name of the sample to be analysed", metavar="character"),
#  make_option(c("-n", "--normalname"), type="character", default=NULL, help="Name of matched normal", metavar="character"),
  make_option(c("--sb"), type="character", default=NULL, help="CEL file of sample to be analysed", metavar="character"),
  make_option(c("--nb"), type="character", default=NULL, help="CEL file of matched normal", metavar="character"),
  make_option(c("--sex"), type="character", default=NULL, help="Sex of the sample", metavar="character"),
  make_option(c("-o", "--output"), type="character", default=NULL, help="Directory where output will be written", metavar="character"),
  make_option(c("--skip_allelecount"), type="logical", default=FALSE, action="store_true", help="Provide when alleles don't have to be counted. This expects allelecount files on disk", metavar="character"),
  make_option(c("--skip_preprocessing"), type="logical", default=FALSE, action="store_true", help="Provide when pre-processing has previously completed. This expects the files on disk", metavar="character"),
  make_option(c("--skip_phasing"), type="logical", default=FALSE, action="store_true", help="Provide when phasing has previously completed. This expects the files on disk", metavar="character"),
  make_option(c("--cpu"), type="numeric", default=8, help="The number of CPU cores to be used by the pipeline (Default: 8)", metavar="character")
)

opt_parser = OptionParser(option_list=option_list)
opt = parse_args(opt_parser)

analysis = opt$analysis_type
SAMPLENAME = opt$samplename
#NORMALNAME = opt$normalname
NORMALCEL = opt$nb
SAMPLECEL = opt$sb
IS.MALE = opt$sex=="male" | opt$sex=="Male"
RUN_DIR = opt$output
SKIP_ALLELECOUNTING = opt$skip_allelecount
SKIP_PREPROCESSING = opt$skip_preprocessing
SKIP_PHASING = opt$skip_phasing
NTHREADS = opt$cpu

# The normalname parameter is not used as the pipeline starts from a single file with both sample of interest and normal in one file, as is dumped from the CEL files
NORMALNAME = NA
###############################################################################
# 2022-08-29
# A pure R Battenberg v3.0.0 SNP6 pipeline implementation.
###############################################################################

# General static
basedir = "/nfs/users/nfs_s/sd11/scratch17_t219/reference/human/battenberg/"
IMPUTEINFOFILE = file.path(basedir, "battenberg_impute_v3/impute_info.txt")
G1000PREFIX = file.path(basedir, "battenberg_1000genomesloci2012_v3/1000genomesAlleles2012_chr")
IMPUTE_EXE = "impute2" # Assumed to be in $PATH

# General SNP6 specific
PROBLEMLOCI = NA
SNP6_REF_INFO_FILE = file.path(basedir, "battenberg_snp6/snp6_ref_info_file.txt")
BIRDSEED_REPORT_FILE = "birdseed.report.txt" # No control over the name of this file, as it is automatically generated by APT within cel2baf.logr

# Link to required dependencies - the below setup assumes these are in $PATH
## download here: https://www.thermofisher.com/de/de/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network/affymetrix-power-tools.html
APT_PROBESET_GENOTYPE_EXE =  "apt-probeset-genotype"
APT_PROBESET_SUMMARIZE_EXE = "apt-probeset-summarize"
## download here: http://www.openbioinformatics.org/penncnv/download/gw6.tar.gz
NORM_GENO_CLUST_EXE = "normalize_affy_geno_cluster.pl"

# Parameters
PLATFORM_GAMMA = 0.55
PHASING_GAMMA = 1
SEGMENTATION_GAMMA = 10
SEGMENTATIIN_KMIN = 3
PHASING_KMIN = 1
CLONALITY_DIST_METRIC = 0
ASCAT_DIST_METRIC = 1
MIN_PLOIDY = 1.6 #1.6
MAX_PLOIDY = 4.8 #4.8
MIN_RHO = 0.13 #0.1
MAX_RHO = 1.02 #1
MIN_GOODNESS_OF_FIT = 0.63
BALANCED_THRESHOLD = 0.51
MIN_NORMAL_DEPTH = 10
CALC_SEG_BAF_OPTION = 1
HETEROZYGOUSFILTER = "none"

# Change to work directory and load the chromosome information
setwd(RUN_DIR)

battenberg(samplename=SAMPLENAME, 
           normalname=NORMALNAME, 
           sample_data_file=SAMPLECEL, 
           normal_data_file=NORMALCEL, 
	   ismale=IS.MALE,
           imputeinfofile=IMPUTEINFOFILE, 
           g1000prefix=G1000PREFIX, 
           problemloci=PROBLEMLOCI, 
           data_type="snp6",
           impute_exe=IMPUTE_EXE,
           nthreads=NTHREADS,
           platform_gamma=PLATFORM_GAMMA,
           phasing_gamma=PHASING_GAMMA,
           segmentation_gamma=SEGMENTATION_GAMMA,
           segmentation_kmin=SEGMENTATIIN_KMIN,
           phasing_kmin=PHASING_KMIN,
           clonality_dist_metric=CLONALITY_DIST_METRIC,
           ascat_dist_metric=ASCAT_DIST_METRIC,
           min_ploidy=MIN_PLOIDY,
           max_ploidy=MAX_PLOIDY,
           min_rho=MIN_RHO,
           min_goodness=MIN_GOODNESS_OF_FIT,
           uninformative_BAF_threshold=BALANCED_THRESHOLD,
           calc_seg_baf_option=CALC_SEG_BAF_OPTION,
           skip_allele_counting=SKIP_ALLELECOUNTING,
           skip_preprocessing=SKIP_PREPROCESSING,
           skip_phasing=SKIP_PHASING,
           snp6_reference_info_file=SNP6_REF_INFO_FILE, 
           apt.probeset.genotype.exe=APT_PROBESET_GENOTYPE_EXE, 
           apt.probeset.summarize.exe=APT_PROBESET_SUMMARIZE_EXE,
           norm.geno.clust.exe=NORM_GENO_CLUST_EXE, 
           birdseed_report_file=BIRDSEED_REPORT_FILE,
           heterozygousFilter=HETEROZYGOUSFILTER,
	   write_battenberg_phasing=FALSE)