call_fings: 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 paths of a pair of matched tumor/normal BAMs and the tumors' VCF. Then it calls FiNGS to calculate metrics based on the BAM files, as well as providing filtering for FP variants called by the variant caller.

Usage

call_fings(
  bin_path = "tools/fings/FiNGS.py",
  bin_path2 = "tools/bcftools/bcftools",
  bin_path3 = "tools/htslib/bgzip",
  bin_path4 = "tools/htslib/tabix",
  tumor_bam = "",
  normal_bam = "",
  tumor_vcf = "",
  ref_genome = "",
  output_dir = "",
  max_depth = 1000,
  pass_in = TRUE,
  pass_out = FALSE,
  verbose = FALSE,
  param = "tools/fings/icgc_filter_parameters.txt"
)

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.
ref_genome	REQUIRED Path to reference genome fasta file.
output_dir	OPTIONAL Path to the output directory.
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.
verbose	OPTIONAL Enables progress messages. Default False.
param	REQUIRED Path to file with filter params.
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
threads	OPTIONAL Number of threads. Default 3

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