8. Quality Control Reports

gemBS creates QC reports for the following analysis steps:

  1. Mapping.

  2. Genotype calling and methylation estimation.

Basic statistics are collected during the analysis and stored in .json format. From those .html and .tex documents are created. It is also possible to generate .pdf reports from the LaTeX documents.

Mapping reports are created once by GEM3 and once by bs_call. This allows the user to get QC statistics if only one component is run and details how the initial alignments (either GEM3 or alternative mapper) are used for variant and methylation calling.

gemBS does not create any QC report for the initial sequencing data, however they can be easily created using FASTQC.

8.1 GEM3 Report

To create the .html or .pdf reports the report subcommand is used. By default this will generate both the mapping and calling report (as well as a summary page linking the two) if the mapping and calling steps have been completed. It is also possible to generate only the mapping or calling report if required.

USAGE:
 gemBS report [FLAGS] [OPTIONS]

FLAGS:
 -P, --pdf        Generate pdf version of QC report (requires latexmk and pdflatex)
 -M, --mapping    Generate mapping report
 -C, --calling    Generate calling report
 -h, --help       Prints help information

OPTIONS:
 -p, --project <NAME>             Output title for report (project name)
 -r, --report-dir <PATH>          Root directory for reports
 -S, --paper-size <PAPER_SIZE>    Select paper size for latex versions of report [possible values: a4, letter]
 -t, --threads <THREADS>          Number of threads for extraction pipeline
 -c, --cores <CORES>              Number of cores for a job (default - available cores / jobs)
 -T, --time <TIME>                Time required for a job
 -m, --memory <MEMORY>            Memory required for a job (default - available memory / jobs)

Parameters:

Section

Key

Description

map

bam_dir

Directory where BAM files were generated

call

bcf_dir

Directory where BCF files were generated

call

project

Project name - used as prefix for output files

call

report_dir

Output directory path

call

paper_size

Paper size for latex versions (a4 or letter)

cores

Number of cores

threads

Number of threads

jobs

Number of parallel jobs

memory

Memory usage

time

Time required

Outputs:

Type

Location

HTML

/report_path/project_name.html

HTML

/report_path/mapping/index.html

HTML

/report_path/calling/index.html

PDF

/report_path/project_name.pdf

Note

Generation of PDF reports requires the installation of TeXLive, which is an optional install.