Generate diagnostic plots for alignment QC checks using Alfred summary files

Single command to generate a comprehensive set of diagnostic plots that assist in performing QC checks of tumor/normal read alignment of various sequencing protocol flavors using Alfred summary files.

Usage

get_qc_diagnostics_alignment(
  path_to_tumor_dir = NULL,
  path_to_normal_dir = NULL,
  dataset_title = "",
  seq_center = "",
  seq_protocol = "WGS",
  output_path = getwd(),
  verbose = T
)

Arguments

path_to_tumor_dir

Path to directory of tumor sample Alfred summary files

path_to_normal_dir

Path to directory of normal sample Alfred summary files

dataset_title

Name of the dataset

seq_center

Institute/site where sequencing was performed

seq_protocol

Type of sequencing protocol for display purposes, default: WGS

output_path

Location to save report PDF, default: getwd()

verbose

Output CLI during workflow, default: TRUE

Value

Patchwork 'quilt'-like plot of ggplots

Examples

# After downloading `*.qc.summary.txt` Alfred output file from the MGP1000 run,
# place tumor and normal sample files into respective subdirectories
# get_qc_diagnostics_alignment(
# path_to_tumor_dir = "data/sanger/examplePDexport_999/preprocessing/alfred/tumor/",
# path_to_normal_dir = "data/sanger/examplePDexport_999/preprocessing/alfred/normal/",
# dataset_title = "examplePDexport_999",
# seq_center = "Wellcome Sanger Institute",
# output_path = "data/sanger/examplePDexport_999/preprocessing/")