IRCC GENE PANEL

This document summarizes procedures for generating IRCC gene panel mutation data output.
Data analysis has been performed by Dr Aikaterini Chatzipli in Ultan McDermott group at the Wellcome Trust Sanger Intitute, UK.

Analysis

• Baits corresponding to a cancer gene panel were designed using SureSelect DNA platform (Agilent genomics).
• 75 pb paired-end Sequencing was done using a HISEQ 2000 v4 system (Illumina).
• The algorithms used for the analysis are the following
  • Bioconductor package XenofilteR was used to separate human from mouse reads interrogating the bam files.
  • Calling for mutations ( substitutions, insertions and deletions) was done using Caveman and Pindel algorithms (versions
    1.5.3 and 4.2, respectively)
  • Calling for Copy Number analysis was done using CNVkit