new_haplotypecaller_gatk: Variant Calling using HaplotypeCaller

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 Calling using HaplotypeCaller

Description

This function functions calls HaplotypeCaller for variant calling. 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

new_haplotypecaller_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,
  bam = NULL,
  region = NULL,
  score = TRUE,
  score_CNN = "CNN_1D",
  filter = TRUE,
  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.
bam	OPTIONAL Path to normal BAM file.
region	REQUIRED Genomic position in samtools format chr:start-end.

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.