Protocol for Mendelian-error based QC
In this project, we will establish an infrastructure and perform QC of genotypic data generated by BGI using Mendelian errors check.
Status: under development
Contributors: Yurii, Lennart, Elisa
Timeline: end Sep 2010 - end Dec 2010
Depends on: availability of VCF data, ChipBasedQcPipeline (soft)
Aims and Deliverables
- Establish custom pipeline for Mendelian-check QC.
- Check quality of sequence data.
- Confirm factors (established in ChipBasedQcPipeline) affecting quality of sequencing.
- Confirm and possibly fine-tune thresholds of quality metrics established in ChipBasedQcPipeline.
- Confirm the false-positive and false-negative rates for variants discovered in our study (established in ChipBasedQcPipeline).
- Explore the potential of improvement of calls by exploiting information from the sequencing of relatives (see TrioAwareVariantDiscoveryPipeline?, TrioAwarePhasingPipeline).
- Estimate the potential for de-novo variant discovery based on phasing information (see DeNovoVariationPipeline)
- In accord with ChipBasedQcPipeline, provide QC'ed data
The basic idea of what questions should be addressed (without saying how) is summarized in MendelianQcPipelineIdea.
Automated workflow (will be) provided in MendelianQcPipelineWorkflow? page.