vcf_format: VCF formating using bcftools

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

Description

This function formats VCF file using bcftools

Usage

vcf_format(
  vcf = "",
  bin_path = "tools/bcftools/bcftools",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
 
    expr = "'%CHROM\\t%POS\\t%ID\\t%REF\\t%ALT\\t%QUAL\\t%FILTER\\t%INFO\\n'",
  verbose = FALSE,
  output_dir = ""
)

Arguments

vcf	Path to vcf file.
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.
expr	Expresion by which to format VCF. Default %CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO\n
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.