call_fings_parallel: Filters SNVs from any variant caller to remove false...

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

Description

This function takes a path to a directory with BAM files and a patient ID. Then it subsets all BAM files specific to the patient, identifying between cancer and normal samples using the germline identifier. It also takes a directory with vcf files and subsets them based on the sample ID. Afterwards, it calls FiNGS to calculates metrics based on BAM files, providing filtering of FP.

Usage

call_fings_parallel(
  bin_path = "tools/FiNGS/fings/FiNGS.py",
  bin_path2 = "tools/bcftools/bcftools",
  bin_path3 = "tools/htslib/bgzip",
  bin_path4 = "tools/htslib/tabix",
  bam_dir = "",
  vcf_dir = "",
  patient_id = "",
  germ_pattern = "GL",
  ref_genome = "",
  max_depth = 1000,
  pass_in = TRUE,
  pass_out = FALSE,
  param = "tools/fings/icgc_filter_parameters.txt",
  threads = 3,
  output_dir = "",
  verbose = FALSE
)

Arguments

bin_path	REQUIRED Path to FiNGS binary. Default tools/FiNGS/fings/FiNGS.py.
bin_path2	REQUIRED Path to bcftools binary. Default tools/bcftools/bcftools.
bin_path3	REQUIRED Path to bgzip binary. Default tools/htslib/bgzip.
bin_path4	REQUIRED Path to tabix binary. Default tools/htslib/tabix.
bam_dir	REQUIRED Path to directory with BAM files.
vcf_dir	REQUIRED Path to directory with VCF files.
patient_id	REQUIRED Patient ID to analyze. Has to be in file names to subselect samples.
germ_pattern	REQUIRED Pattern used to identify germline samples. Ex GL
ref_genome	REQUIRED Path to reference genome fasta file.
max_depth	OPTIONAL Maximum number of reads.Reads beyond this depth will be ignored
pass_in	OPTIONAL Only input variants with a PASS. Default TRUE.
pass_out	OPTIONAL Only output variants with a PASS. Default FALSE.
param	REQUIRED Path to file with filter params.
threads	OPTIONAL Number of threads. Default 3
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.

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