call_platypus: Variant calling using Platypus

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

Description

This function calls somatic variants in a pair of tumor-normal matched samples, or just in a tumor sample if no matched sample is available.

Usage

call_platypus(
  bin_path = "tools/platypus/Platypus.py",
  bin_path2 = "tools/bcftools/bcftools",
  bin_path3 = "tools/htslib/bgzip",
  bin_path4 = "tools/htslib/tabix",
  tumor_bam = "",
  normal_bam = "",
  ref_genome = "",
  vcf_overlay = "",
  output_dir = "",
  verbose = FALSE,
  threads = 3,
  output_name = "",
  targeted = FALSE
)

Arguments

bin_path	REQUIRED Path to fastQC executable. Default path tools/platypus/Platypus.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.
tumor_bam	REQUIRED Path to tumor bam file.
normal_bam	REQUIRED Path to germline bam file.
ref_genome	REQUIRED Path to reference genome fasta file.
vcf_overlay	REQUIRED Path to vcf overlay to use as source.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
threads	OPTIONAL Number of threads to use. Default 3.
output_name	OPTIONAL Name for the output. If not given the name of the first sample in alphanumerical order will be used.
targeted	OPTIONAL Sequencing data is exome/targeted. Default FALSE

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