generate_sets: Generate a 1:n sets between a group of vcfs

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

Description

This function takes a path to either a vcf file or to a directory of vcf files and outputs an inset/outset between these vcf files.

Usage

generate_sets(
  bin_path = "tools/bcftools/bcftools",
  vcf = "",
  vcf_dir = "",
  filter = "PASS",
  output_dir = "",
  set_names = "",
  verbose = FALSE,
  threads = 3,
  plot = TRUE
)

Arguments

bin_path	REQUIRED Path to bcftools binary. Default tools/bcftools/bcftools
vcf	OPTIONAL Path to a single vcf file or a vector of vcf files. Only if vcf_dir is not given.
vcf_dir	OPTIONAL Path to a directory with vcf files to generate a set for. Only if vcf is not given.
filter	OPTIONAL Filter variants by. Default PASS
output_dir	OPTIONAL Path to output directory. Default current directory
set_names	OPTIONAL Names to use to identify each set.
verbose	Optional Enables progress messages. Default False.
threads	OPTIONAL Number of threads to use. Default 3
plot	OPTIONAL Generate a VennDiagram plot with set intersections

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