CNNScoreVariants: Annotate a VCF with scores from a Convolutional Neural...

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

Description

This function takes a vcf and then annotates it with CNN scores. If a BAM files is supplied a 2D model will be applied, otherwise a 1D model will be applied.

Usage

CNNScoreVariants(
  bin_path = "tools/gatk/gatk",
  vcf = "",
  ref_genome = "",
  bam = "",
  output_dir = "",
  output_name = "",
  verbose = FALSE
)

Arguments

bin_path	REQUIRED Path to GATK binary. Default tools/gatk/gatk
vcf	REQUIRED Path to VCF file to annotate.
ref_genome	REQUIRED Path to reference genome.
bam	OPTIONAL Path to BAM file.
output_dir	OPTIONAL Path to BAM file.
output_name	OPTIONAL Default output name. If not supplied it will use the vcf file name.
verbose	OPTIONAL Enables progress messages. Default False.

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