filter_variant_tranches_gatk: Variant Trench Filtering using GATK

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

Variant Trench Filtering using GATK

Description

This function filters variant tranches calls generated using CNNScoreVariants method

Usage

filter_variant_tranches_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,
  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.
indel_db	OPTIONAL Path to database with indel info.
haplotype_db	OPTIONAL Path to database with haplotype info.
vcf	REQUIRED Path to VCF file.
info_key	OPTIONAL Info Key for CNN model training. Default CNN_1D. Options "CNN_1D","CNN_2D"
snp_tranche	OPTIONAL SNP tranche cut-off.
indel_tranche	OPTIONAL INDEL tranche cut-off.
keep_previous_tranche	OPTIONAL Remove previous filter information.

Details

For more information read: https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches

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