This function takes preprocessed data and performs haplotype reconstruction.
run_haplotyping(
chrom,
tumourname,
normalname,
ismale,
imputeinfofile,
problemloci,
impute_exe,
min_normal_depth,
chrom_names,
externalhaplotypeprefix = NA,
use_previous_imputation = F,
snp6_reference_info_file = NA,
heterozygousFilter = NA,
usebeagle = FALSE,
beaglejar = NA,
beagleref = NA,
beagleplink = NA,
beaglemaxmem = 10,
beaglenthreads = 1,
beaglewindow = 40,
beagleoverlap = 4,
javajre = "java"
)The chromosome for which to reconstruct haplotypes
Identifier of the tumour, used to match data files on disk
Identifier of the normal, used to match data files on disk
Boolean, set to TRUE if the sample is male
Full path to the imputeinfo reference file
Full path to the problematic loci reference file
Path to the impute executable (can be found if its in $PATH)
Minimal depth in the matched normal required for a SNP to be used
A vector containing the names of chromosomes to be included
SNP6 only parameter Default: NA
SNP6 only parameter Default: NA
Should use beagle5 instead of impute2 Default: FALSE
Full path to Beagle java jar file Default: NA
Full path to Beagle reference file Default: NA
Full path to Beagle plink file Default: NA
Integer Beagle max heap size in Gb Default: 10
Integer number of threads used by beagle5 Default:1
Integer size of the genomic window for beagle5 (cM) Default:40
Integer size of the overlap between windows beagle5 Default:4
Path to the Java JRE executable (default java, i.e. in $PATH)