call_bcftools_parallel: Variant calling using bcftools on parallel per genomic region

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

Description

This function calls SNPs in a sample

This function calls SNPs in a sample

Usage

call_bcftools_parallel(
  bin_path = "tools/bcftools/bcftools",
  bam = "",
  ref_genome = "",
  output_dir = "",
  region_bed = "",
  threads = 3,
  verbose = FALSE
)

call_bcftools_parallel(
  bin_path = "tools/bcftools/bcftools",
  bam = "",
  ref_genome = "",
  output_dir = "",
  region_bed = "",
  threads = 3,
  verbose = FALSE
)

Arguments

bin_path	Required Path to bcftools binary. Default path tools/bcftools/bcftools.
bam	Required Path to bam file.
ref_genome	Path to reference genome fasta file.
output_dir	Path to the output directory.
region_bed	Path to bed file with regions to analyze.
threads	Optional Number of threads. Default 3
verbose	Enables progress messages. Default False.

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