Input/Output

Input

Sample config file

Sample identifier and their necessary filepaths (bam, vcf, etc.) are provided to QuaC in a tsv formatted config file via --sample_config. Columns required depend on the flags supplied to src/run_quac.py. This table lists the allowed columns and when to use them.

Column	When to use	Description
sample_id	Always	Sample identifier
bam	Always	BAM filepath
vcf	Always	VCF filepath
capture_bed	--exome	Capture region bed filepath
fastqc_raw	--include_prior_qc	Filepath to FastQC zip files created from raw fastqs. Use comma as delimiter if multiple files.
fastqc_trimmed	--include_prior_qc	Filepath to FastQC zip files created from trimmed fastqs. Use comma as delimiter if multiple files.
fastq_screen	--include_prior_qc	Filepath to FastQ Screen txt files. Use comma as delimiter if multiple files.
dedup	--include_prior_qc	Filepath to Picard's MarkDuplicates txt files. Use comma as delimiter if multiple files.
multiqc_rename_config	--allow_sample_renaming	Filepath to label rename configfile to use with multiqc

Refer to our system testing directory for example sample config files at .test/configs. For example:

• .test/configs/no_priorQC/sample_config/project_2samples_wgs.tsv - Sample config file for WGS samples and no prior QC.
• .test/configs/no_priorQC/sample_config/project_2samples_exome.tsv - Sample config file for exome samples and no prior QC. Note that WGS and exome samples can't be used in the same config file.
• .test/configs/include_priorQC/sample_config/project_2samples_wgs.tsv - Sample config file for WGS samples with prior QC data available from certain QC tools.

Pedigree file

QuaC requires a pedigree file as input via --pedigree. Samples listed in this file must correspond to those in sample config file (--sample_config).

Output

QuaC results are stored at the path specified via option --outdir (default: data/quac/results/test_project/analysis). Refer to the system testing's output to learn more about the output directory structure.

QC output are stored at the sample level as well as the project level (ie. all samples considered together) depending on the type of QC run. For example, Qualimap tool is run at the sample level whereas Somalier tool is run at the project level. MultiQC reports are available both at the sample and project level.