cnn_score_variants_gatk: Germline Variant Scoring Using CNN

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Germline Variant Scoring Using CNN

Description

This function functions calls CNNScoreVariants. If a vector of normal samples are provided these will be processed in multi-sample mode. To run in normal mode suppply a single normal sample. TO DO// Implement mitochondrial mode feature

Usage

cnn_score_variants_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  indel_db = build_default_reference_list()$HG19$variant$mills_reference,
  haplotype_db = build_default_reference_list()$HG19$variant$hapmap_reference,
  vcf = NULL,
  bam = NULL,
  filter = TRUE,
  info_key = "CNN_1D",
  snp_tranche = 99.95,
  indel_tranche = 99.4,
  keep_previous_filters = FALSE,
  ...
)

Arguments

sif_gatk	REQUIRED Path to gatk sif file.
ref_genome	REQUIRED Path to reference genome fasta file.
vcf	REQUIRE Path to VCF file.
bam	OPTIONAL Path to BAM file. If given then 2D CNN will be applied

Details

For more information read: https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.