vcf_filter_variants: VCF filtering using bcftools

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

Description

This function filters VCF calls using bcftools

Usage

vcf_filter_variants(
  unfil_vcf = "",
  bin_path = "tools/bcftools/bcftools",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  qual = 30,
  mq = 40,
  state = "",
  ref = "",
  type = "",
  filter = "",
  verbose = FALSE,
  output_dir = ""
)

Arguments

unfil_vcf	Path to unfiltered 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.
qual	Quality filter. Default 30.
mq	Mapping quality filter. Default 40.
state	Optional Variant state to select. Options: het/homo
ref	Optional Filter variants with ID.
type	Optional Variant type to include. Options: snp/indel. Default includes both
filter	Optional Filter to include Options: PASS/.
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.