Proposed Quality Control.

Pre-alignment:

• Duplicate input checking.
• Quality scores histogram from the BGI.
  • Maybe other graphs/data provided by the BGI.
• Quality scores with the FastqC toolkit.
  • GC content.
  • Quality scores per base.
  • Quality scores per read.
  • N-content.
  • Length distribution.
  • Over representation of reads.
  • A summary of this data provided by a script.

Alignment:

• Percentage aligned.
• Insert size distribution.
• Coverage.
  • Distribution.
  • Visualisation as a wiggle track.
    • Intra sample distance calculation of the wiggle tracks.
• Mapping quality distribution.
• Look into Picard Tools.

Recalibration:

• Any available statistics from GATK?

Variant calling:

• Transition / transversion rate.
• X, Y coverage (check encoding of sample tags).
• Mutation rate.
  • Autosomal.
  • Y.
  • M.
• Distribution of SNPs found in dnSNP.
• Indel / substitution rate.
• Cross check with immuno-chip.

In all steps, cross check with the data provided by the BGI.