vcf_sets: Generate a set between a group of vcfs usign bcftools

Description Usage Arguments

View source: R/util.R

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

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vcf_sets(
  bin_path = "tools/bcftools/bcftools",
  vcf = "",
  vcf_dir = "",
  set_formula = "=+2",
  filter = "PASS",
  output_dir = "",
  verbose = FALSE
)

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.

set_formula

REQUIRED Formula to filter variants. Default =+2.

filter

OPTIONAL Filter variants by. Default PASS

output_dir

OPTIONAL Path to output directory. Default current directory

verbose

Optional Enables progress messages. Default False.


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