process_variants: Process variants generated using variant_call and...

In TearsWillFall/variantCall: An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

Description

Process variants generated using variant_call and variant_call_strelka functions This function takes the output directory of variant_call function and processes the variants accordingly.

Usage

process_variants(
  bin_path = "tools/ensembl-vep/vep",
  bin_path2 = "tools/ensembl-vep/filter_vep",
  bin_path3 = "tools/bcftools/bcftools",
  bin_path4 = "tools/htslib/bgzip",
  bin_path5 = "tools/htslib/tabix",
  bin_path6 = "tools/vcf2maf/vcf2maf.pl",
  var_dir = "",
  bed_snps = "",
  ref_genome = "",
  output_dir = "",
  germ_pattern = "GL",
  vep_data = "~/.vep",
  verbose = FALSE,
  threads = 3
)

Arguments

bin_path	REQUIRED Path to vep binary. Default tools/ensembl-vep/vep
bin_path2	REQUIRED Path to vep filter binary. Default tools/ensembl-vep/filter_vep
bin_path3	REQUIRED Path to bcftools binary. Default tools/bcftools/bcftools
bin_path4	REQUIRED Path to bgzip. Default tools/htslib/bgzip
bin_path5	REQUIRED Path to vaf2maf. Default tools/vaf2maf/vaf2maf.pl
var_dir	REQUIRED Path to variant directory.
bed_snps	REQUIRED Path to BED with Panel SNPs
output_dir	OPTIONAL Path to the output directory.
germ_pattern	OPTIONAL Pattern for normale samples
vep_data	REQUIRED Path to VEP data directory.
verbose	DEFAULT==FALSE Enables progress messages.
threads	OPTIONAL Number of threads per job. Default 3

TearsWillFall/variantCall documentation built on Oct. 15, 2021, 8:51 p.m.