CNV Analysis Toolkit Documentation

Introduction

The CNV analysis toolkit was first designed to accomodate the needs of a specific project that used monozygotic twins quartets in order to assess the efficiency of different CNV genotyping methods. This software has been made publicly available for transparency related matters and in the hope that some utilities be useful in similar studies.

Contents

• The bed utility to generate UCSC bed files
• The cnv_counter utility to count the number of CNVs corresponding to a given criterion
• cnv_db: DGV database interface
  • cnv_db.db
• cnv_struct: A data structure to handle CNVs
• compare_dgv script to check DGV overlap
• de_novo_germinal tool to filter out de novo variants
• generate_cnv_graph a data structure to handle different CNV signatures in a family
• mendelian: Tools to filter inherited CNVs
• merge_cnvs: Merges adjacent variants (fragmentation)
• parsers for the different calling algorithms
  • parsers.breakdancer
  • parsers.cnver
  • parsers.cnvnator
  • parsers.cnvpickle
  • parsers.erds
  • parsers.omni25
• plot_cnv_size_dgv_ro: Tool to plot the reciprocal overlap to DGV as a function of CNV size
• plot_cnv_size_distribution: Tool to compute the size histogram
• plot_distance_distribution: Tool to represent the distance between adjacent CNVs
• plot_ro: Tool to plot the distribution of the reciprocal overlap between the twins for a dataset
• plot_size_doc_scatter: Tool to plot the depth of coverage information as a function of CNV size
• samples_db creates and queries a database containing of familial statuses and mean coverage.
• validation: a module used for command line arguments validation
• venn: Tools to create Venn diagrams.

Indices and tables

• Index
• Module Index
• Search Page