format_PM_data: Format vcf for downstream point mutatation analysis.

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

Description

This function takes a VCF file and outputs a tab delimited file with data for downstream analysis in CLONETv2 point mutations analysis.

Usage

format_PM_data(
  bin_path = "tools/bcftools/bcftools",
  vcf_dir = "",
  pattern = "",
  vcf = "",
  worst = FALSE,
  output_dir = "",
  output_name = "",
  verbose = FALSE
)

Arguments

bin_path	REQUIRED Path to ASEQ binary. Default tools/bcftools/bcftools
vcf_dir	REQUIRED Path to vcf file directory.
pattern	OPTIONAL Pattern to filter vcfs by.
vcf	OPTIONAL Path to vcf file. Only if vcf directory not provided.
worst	OPTIONAL Only keep the variants with the worst outcome.
output_dir	OPTIONAL Path to the output directory.
output_name	OPTIONAL Name of output file.
verbose	OPTIONAL Enables progress messages. Default False.

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