format_SNP_data: This function filter and formats heterozygous SNP data for...

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 of a directory of unfiltered VCFs files generated using Platypus and the a path of the directory of BAMs from which those VCFs were generated.

Usage

format_SNP_data(
  bin_path = "tools/bcftools/bcftools",
  bin_path2 = "tools/htslib/bgzip",
  bin_path3 = "tools/htslib/tabix",
  bin_path4 = "tools/ASEQ/binaries/linux64/ASEQ",
  unfil_vcf = "",
  unfil_vcf_dir = "",
  bam_dir = "",
  germ_pattern = "GL",
  qual = 30,
  mq = 40,
  min_cov = 20,
  patient_id = "",
  verbose = FALSE,
  output_dir = "",
  jobs = 1,
  threads = 3,
  remove_tmp = TRUE
)

Arguments

bin_path	Path to bcftools binary. Default tools/bcftools/bcftools.
bin_path2	Path to bgzip binary. Default tools/htslib/bgzip.
bin_path3	Path to tabix binary. Default tools/htslib/tabix.
bin_path4	Path to ASEQ binary. Default tools/ASEQ/binaries/linux64/ASEQ
unfil_vcf	Path to unfiltered VCF file.
unfil_vcf_dir	Path to unfiltered VCF file directory.
bam_dir	Path to BAM file directory.
germ_pattern	Germline identifier.
qual	Quality filter. Default 30.
mq	Mapping quality filter. Default 40.
min_cov	Minimum coverage to filter. Default 20.
patient_id	Patient identifier.
verbose	Enables progress messages. Default FALSE.
output_dir	Path to the output directory.
jobs	Number of jobs to do in parallel. Default 1
threads	Number of threads to use per job. Default 3
remove_tmp	Remove temporary files. Default TRUE

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