fix_mnps: VCF fix MNPs

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

Description

Exclude MNPs from vcf file

Usage

fix_mnps(
  vcf = "",
  bin_path = "tools/bcftools/bcftools",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  verbose = FALSE,
  output_dir = ""
)

Arguments

vcf	Path to unfiltered vcf file.
bin_path	Path to bcftools binary. Default tools/bcftools/bcftools.
bin_path2	Path to bgzip binary. Default tools/htslib/bgzip.
bin_path3	Path to tabix binary. Default tools/htslib/tabix.
verbose	Enables progress messages. Default False.
output_dir	Path to the output directory.

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