call_HaplotypeCaller: Wrapper for GATK HaplotypeCaller for Germline Variant calling

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.Cuttently only single sample implementation

Usage

call_HaplotypeCaller(
  bin_path = "tools/gatk/gatk",
  bin_path2 = "tools/bcftools/bcftools",
  bin_path3 = "tools/htslib/bgzip",
  bin_path4 = "tools/htslib/tabix",
  normal_bam = "",
  ref_genome = "",
  region = "",
  output_dir = "",
  resources = "",
  patient_id = "",
  info_key = "CNN_1D",
  snp_tranche = 99.95,
  indel_tranche = 99.4,
  keep_previous_filters = FALSE,
  verbose = FALSE,
  threads = 3
)

Arguments

bin_path	REQUIRED Path to GATK binary. Default tools/gatk/gatk
bin_path2	Path to bcftools binary. Default tools/bcftools/bcftools.
bin_path3	Path to bgzip binary. Default tools/htslib/bgzip.
bin_path4	Path to tabix binary. Default tools/htslib/tabix.
normal_bam	REQUIRED Path to BAM file
ref_genome	REQUIRED Path to reference genome
region	OPTIONAL Genomic region/regions to analyze. In samtools format.
output_dir	OPTIONAL Path to output dir
resources	OPTIONAL Path to resources for variant filtering
patient_id	OPTIONAL Patient ID after which to name the output. If not given bam file name will be used.
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
keep_previous_filters	OPTIONAL Keep previous filters in VCF. Default False
verbose	Optional Enables progress messages. Default False
threads	OPTIONAL Number of threads per job. Default 3
output_name	OPTIONAL Name of the sample to output

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