detGeneStatuses: Determine gene amplifications and biallelic losses

In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output

Description

Determine gene amplifications and biallelic losses

Usage

detGeneStatuses(
  out.dir,
  input.file.paths = c(germ_vcf = "", som_vcf = "", gene_cnv = "", cnv = ""),
  sample.name,
  bed.file = BED_FILE,
  java.path = JAVA_PATH,
  snpsift.path = SNPSIFT_PATH,
  chrom.arm.split.method = "hmf",
  do.snpeff.ann = F,
  verbose = T
)

Arguments

out.dir	Path to output dir
input.file.paths	A list or vector supplying the path output files from the HMF pipeline.
sample.name	Name of the sample This list should be in the form c(germ_vcf=”, som_vcf=”, gene_cnv=”, cnv=”)
bed.file	Path to the bed file containing the genes of interest. This bed file should also contain the column ensembl_gene_id
java.path	Path the the java binary
snpsift.path	Path to the SnpSift jar
chrom.arm.split.method	Can be 'hmf' or 'gap'. Refer to documentation for calcChromArmPloidies().
do.snpeff.ann	Annotate SNV/indels variant type with snpeff?
verbose	Show progress messages?

Value

Writes a diplotypes table to the output dir

luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.