vcf_annotate: VCF annotation using bcftools

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

Description

This function annotates VCF file using bcftools

Usage

vcf_annotate(
  bin_path = "tools/bcftools/bcftools",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  vcf = "",
  db = "",
  verbose = FALSE,
  output_dir = "",
  threads = 1
)

Arguments

bin_path	Path to gatk binary. Default tools/gatk/gatk.
bin_path2	Path to bgzip binary. Default tools/htslib/bgzip.
bin_path3	Path to tabix binary. Default tools/htslib/tabix.
vcf	Path to vcf file.
db	Path to vcf file with SNPs database.
verbose	Enables progress messages. Default False.
output_dir	Path to the output directory.
threads	Additional in/out compression threads. Default 1.
state	Variant state. Default het.

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