parse.aggregated.mut: Parse the VCF file to aggregate variants by genes and...

In liliulab/gust: Genes Under Selection In Tumors

Parse the VCF file to aggregate variants by genes and mutation types

Description

Parse the VCF file to aggregate variants by genes and mutation types

Usage

parse.aggregated.mut(input.file.name, output.folder = "",
  output.prefix = "")

Arguments

input.file.name:	A VCF-formatted file to read SnpEff annotated somatic variants. This input file shall contain these fields: Tumor_Sample_Barcode, Chromosome, Start_Position, dbSNP_RS, Reference_Allele, Tumor_Seq_Allele2, FILTER, One_Consequence, Hugo_Symbol, Gene, Feature, ENSP, HGVSc, HGVSp_Short, Amino_acids, Codons, ENSP, RefSeq, Entrez_Gene_Id.
output.folder:	the folder to write output files
output.prefix:	prefix used to name the output files. Output files include prefix.error.txt (mutations cannot be mapped), prefix.mut.filtered.txt (somatic variants with matching types, prefix.mut.cnt.txt (somatic variants aggregated by sample, gene and mutational type), prefix.mut.summary.txt (somatic variants aggregated by gene and mutational type across all samples), prefix.symbol_2_cds_id.txt (mapping gene symbols to ensembl transcript ids), and prefix.log.txt (log information).

Examples

parse.aggregated.mut(input.file.name='./examples/TCGA.ACC.mutect.somatic.maf.gz', output.folder='./examples/', output.prefix='TCGA.ACC')

liliulab/gust documentation built on Sept. 29, 2024, 2:52 p.m.