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

battenberg

R Documentation

Run the Battenberg pipeline

Description

Run the Battenberg pipeline

Usage

battenberg(
  tumourname,
  normalname,
  tumour_data_file,
  normal_data_file,
  imputeinfofile,
  g1000prefix,
  problemloci,
  gccorrectprefix = NULL,
  repliccorrectprefix = NULL,
  g1000allelesprefix = NA,
  ismale = NA,
  data_type = "wgs",
  impute_exe = "impute2",
  allelecounter_exe = "alleleCounter",
  nthreads = 8,
  platform_gamma = 1,
  phasing_gamma = 1,
  segmentation_gamma = 10,
  segmentation_kmin = 3,
  phasing_kmin = 1,
  clonality_dist_metric = 0,
  ascat_dist_metric = 1,
  min_ploidy = 1.6,
  max_ploidy = 4.8,
  min_rho = 0.1,
  min_goodness = 0.63,
  uninformative_BAF_threshold = 0.51,
  min_normal_depth = 10,
  min_base_qual = 20,
  min_map_qual = 35,
  calc_seg_baf_option = 3,
  skip_allele_counting = F,
  skip_preprocessing = F,
  skip_phasing = F,
  externalhaplotypefile = NA,
  usebeagle = FALSE,
  beaglejar = NA,
  beagleref.template = NA,
  beagleplink.template = NA,
  beaglemaxmem = 10,
  beaglenthreads = 1,
  beaglewindow = 40,
  beagleoverlap = 4,
  javajre = "java",
  write_battenberg_phasing = T,
  multisample_relative_weight_balanced = 0.25,
  multisample_maxlag = 100,
  segmentation_gamma_multisample = 5,
  snp6_reference_info_file = NA,
  apt.probeset.genotype.exe = "apt-probeset-genotype",
  apt.probeset.summarize.exe = "apt-probeset-summarize",
  norm.geno.clust.exe = "normalize_affy_geno_cluster.pl",
  birdseed_report_file = "birdseed.report.txt",
  heterozygousFilter = "none",
  prior_breakpoints_file = NULL,
  GENOMEBUILD = "hg19"
)

Arguments

`tumourname`	Tumour identifier, this is used as a prefix for the output files. If allele counts are supplied separately, they are expected to have this identifier as prefix.
`normalname`	Matched normal identifier, this is used as a prefix for the output files. If allele counts are supplied separately, they are expected to have this identifier as prefix.
`tumour_data_file`	A BAM or CEL file for the tumour
`normal_data_file`	A BAM or CEL file for the normal
`imputeinfofile`	Full path to a Battenberg impute info file with pointers to Impute2 reference data
`g1000prefix`	Full prefix path to 1000 Genomes SNP loci data, as part of the Battenberg reference data
`problemloci`	Full path to a problem loci file that contains SNP loci that should be filtered out
`gccorrectprefix`	Full prefix path to GC content files, as part of the Battenberg reference data, not required for SNP6 data (Default: NULL)
`repliccorrectprefix`	Full prefix path to replication timing files, as part of the Battenberg reference data, not required for SNP6 data (Default: NULL)
`g1000allelesprefix`	Full prefix path to 1000 Genomes SNP alleles data, as part of the Battenberg reference data, not required for SNP6 data (Default: NA)
`ismale`	A boolean set to TRUE if the donor is male, set to FALSE if female, not required for SNP6 data (Default: NA)
`data_type`	String that contains either wgs or snp6 depending on the supplied input data (Default: wgs)
`impute_exe`	Pointer to the Impute2 executable (Default: impute2, i.e. expected in $PATH)
`allelecounter_exe`	Pointer to the alleleCounter executable (Default: alleleCounter, i.e. expected in $PATH)
`nthreads`	The number of concurrent processes to use while running the Battenberg pipeline (Default: 8)
`platform_gamma`	Platform scaling factor, suggestions are set to 1 for wgs and to 0.55 for snp6 (Default: 1)
`phasing_gamma`	Gamma parameter used when correcting phasing mistakes (Default: 1)
`segmentation_gamma`	The gamma parameter controls the size of the penalty of starting a new segment during segmentation. It is therefore the key parameter for controlling the number of segments (Default: 10)
`segmentation_kmin`	Kmin represents the minimum number of probes/SNPs that a segment should consist of (Default: 3)
`phasing_kmin`	Kmin used when correcting for phasing mistakes (Default: 3)
`clonality_dist_metric`	Distance metric to use when choosing purity/ploidy combinations (Default: 0)
`ascat_dist_metric`	Distance metric to use when choosing purity/ploidy combinations (Default: 1)
`min_ploidy`	Minimum ploidy to be considered (Default: 1.6)
`max_ploidy`	Maximum ploidy to be considered (Default: 4.8)
`min_rho`	Minimum purity to be considered (Default: 0.1)
`min_goodness`	Minimum goodness of fit required for a purity/ploidy combination to be accepted as a solution (Default: 0.63)
`uninformative_BAF_threshold`	The threshold beyond which BAF becomes uninformative (Default: 0.51)
`min_normal_depth`	Minimum depth required in the matched normal for a SNP to be considered as part of the wgs analysis (Default: 10)
`min_base_qual`	Minimum base quality required for a read to be counted when allele counting (Default: 20)
`min_map_qual`	Minimum mapping quality required for a read to be counted when allele counting (Default: 35)
`calc_seg_baf_option`	Sets way to calculate BAF per segment: 1=mean, 2=median, 3=ifelse median==0 \| 1, mean, median (Default: 3)
`skip_allele_counting`	Provide TRUE when allele counting can be skipped (i.e. its already done) (Default: FALSE)
`skip_preprocessing`	Provide TRUE when preprocessing is already complete (Default: FALSE)
`skip_phasing`	Provide TRUE when phasing is already complete (Default: FALSE)
`externalhaplotypefile`	Vcf containing externally obtained haplotype blocks (Default: NA)
`usebeagle`	Should use beagle5 instead of impute2 Default: FALSE
`beaglejar`	Full path to Beagle java jar file Default: NA
`beagleref.template`	Full path template to Beagle reference files where the chromosome is replaced by 'CHROMNAME' Default: NA
`beagleplink.template`	Full path template to Beagle plink files where the chromosome is replaced by 'CHROMNAME' Default: NA
`beaglemaxmem`	Integer Beagle max heap size in Gb Default: 10
`beaglenthreads`	Integer number of threads used by beagle5 Default:1
`beaglewindow`	Integer size of the genomic window for beagle5 (cM) Default:40
`beagleoverlap`	Integer size of the overlap between windows beagle5 Default:4
`javajre`	Path to the Java JRE executable, only required for haplotype reconstruction with Beagle (default java, i.e. in $PATH)
`write_battenberg_phasing`	Write the Battenberg phasing results as vcf to disk, e.g. for multisample cases (Default: TRUE)
`multisample_relative_weight_balanced`	Relative weight to give to haplotype info from a sample without allelic imbalance in the region (Default: 0.25)
`multisample_maxlag`	Maximal number of upstream SNPs used in the multisample haplotyping to inform the haplotype at another SNP (Default: 100)
`segmentation_gamma_multisample`	The gamma parameter controls the size of the penalty of starting a new segment during mutlisample segmentation. It is the key parameter for controlling the number of segments (Default: 10)
`snp6_reference_info_file`	Reference files for the SNP6 pipeline only (Default: NA)
`apt.probeset.genotype.exe`	Helper tool for extracting data from CEL files, SNP6 pipeline only (Default: apt-probeset-genotype)
`apt.probeset.summarize.exe`	Helper tool for extracting data from CEL files, SNP6 pipeline only (Default: apt-probeset-summarize)
`norm.geno.clust.exe`	Helper tool for extracting data from CEL files, SNP6 pipeline only (Default: normalize_affy_geno_cluster.pl)
`birdseed_report_file`	Sex inference output file, SNP6 pipeline only (Default: birdseed.report.txt)
`heterozygousFilter`	Legacy option to set a heterozygous SNP filter, SNP6 pipeline only (Default: "none")
`prior_breakpoints_file`	A two column file with prior breakpoints to be used during segmentation (Default: NULL)
`GENOMEBUILD`	Genome build upon which the 1000G SNP coordinates were obtained (Default: hg19; options: "hg19" or "hg38")