filter_VEP: Filter VEP results

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

Description

This function filters VCFs generated by VEP

Usage

filter_VEP(
  bin_path = "tools/ensembl-vep/filter_vep",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  unf_vcf = "",
  filter = "",
  verbose = FALSE,
  output_dir = ""
)

Arguments

bin_path	Path to vep binary. Default tools/ensembl-vep/filter_vep.
bin_path2	Path to bgzip binary. Default tools/htslib/bgzip.
bin_path3	Path to tabix binary. Default tools/htslib/tabix.
unf_vcf	Path to vcf file.
filter	Column tags to filter by. Examples "(MAX_AF < 0.01 or not MAX_AF) and FILTER = PASS and SYMBOL in /home/regmova/PCFselect/Panel_V2/PANEL_GENE.txt". For more information check VEP filter info.
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.