* Creates QuaC workflow, which can run somalier, mosdepth, indexcov, covviz and verifybamid2
* Uses pedigree file as input
* Makes it production ready.
* Creates QuaC workflow, which can run somalier, mosdepth, indexcov, covviz and verifybamid2
* Uses pedigree file as input
* Makes it production ready.
2021-05-28 Manavalan Gajapathy
* 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.
* 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, 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.
