v1.0

• QuaC is heavily reworked to be a companion pipeline to small variant caller pipeline and will now perform most of the QC analyses for WGS/WES data. While the small caller pipeline will still run few QC tools (for pragmatic reasons), QuaC will now take over the heavylifting of QC, including the QC-checkup, which is now called as QuaC-Watch.
• Runs in containerized environment using Singularity.
• QuaC can perform both sample-level and project-level QC. This is the major reason why it was decided to separate QC from small-variant caller pipeline, as it could only perform single-sample QC.
• More QC tools were added
• For QC checkup (ie. QuaC-Watch), QuaC now heavily expands to vcf metrics and adds significant amount of QC thresholds for bam metrics.
• QuaC's input are output from the small variant caller pipeline, and former's output will fit seemlessly with the latter's output.
• QuaC accepts pedigree file as input. A dummy pedigree file creator script is provided, which will be handy until phenotips is made available to us.
• System-level testing is added