MendelianQcPipeline

Check for Mendelian inconsistencies exploiting trio structure of the sample.

This is phase 1 project

This work package aims to:

• 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 TrioAwarePhasingPipeline).
• Estimate the potential for de-novo variant discovery based on phasing information (see DeNovoVariationPipeline)

Detailed workflow is summarized in a separate (protocol) document (link will be made from here when available).

Estimated costs for pilot data check and establishing the pipeline: 3 months of BI/data manager/programmer at 1.0 fte + experienced supervisor at 0.1 fte.

Suggested timeline: end of September – end of December

Depends on: availability of VCF pilot data, Chip QC (soft)

Other projects depending on this: QC’ed data (hard)

Major deliverables of phase 1

• Custom pipeline for Mendelian-error based QC
• QC’ed sequence data (also depends on ChipBasedQcPipeline); these data will serve as an input for call improvement, phasing, novel variants, population genetics (variants) and functional variants projects

Note that after completion of phase 1, preliminary phasing can be done using available [ population-based software (e.g. IMPUTE, MACH, BIMBAM), with haplotypes serving as input for imputations project]​[YA2] .