get_pileup_summary: BAM pileup summary for known sites using GATK

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

Description

This function generates a pileup summary that is further used in estimating contamination

Usage

get_pileup_summary(
  bam = "",
  bin_path = "tools/gatk/gatk",
  db = "",
  interval = "",
  verbose = FALSE,
  output_dir = ""
)

Arguments

bam	REQUIRED Path to BAM file.
bin_path	REQUIRED Path to gatk binary. Default tools/gatk/gatk.
db	REQUIRED Path to vcf with known variants.
interval	REQUIRED Path to vcf with intervals to analyze.
verbose	OPTIONAL Enables progress messages. Default False.
output_dir	OPTIONAL Path to the output directory.

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