FilterVariantTranches: Filter Variant Tranches (Mutect2)

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

Description

This function takes an annotated VCF with CNN_D1 or CNN_D2 scores and filter the variants based on set threshold.

Usage

FilterVariantTranches(
  bin_path = "tools/gatk/gatk",
  vcf = "",
  resources = "",
  output_name = "",
  info_key = "CNN_1D",
  snp_tranche = 99.95,
  indel_tranche = 99.4,
  output_dir = "",
  keep_previous_filters = FALSE,
  verbose = FALSE
)

Arguments

bin_path	REQUIRED Path to GATK binary. Default tools/gatk/gatk
vcf	REQUIRED Path to annotated VCF with CNN_D1/CNN_D2 scores
resources	OPTIONAL Path to resources for variant filtering
output_name	OPTIONAL Name of the sample to output
info_key	OPTIONAL Annotation column to select. Default CNN_D1
snp_tranche	OPTIONAL SNP tranche filter value. Default 99.95
indel_tranche	OPTIONAL Indel tranche filter value. Default 99.4
output_dir	OPTIONAL Path to output dir
keep_previous_filters	OPTIONAL Keep previous filters in VCF. Default False
verbose	Optional Enables progress messages. Default False

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