Release 2.0.

MIP is a pipeline for clinical analysis of whole exome and whole genome sequence data.

Contents:

• MIP - Mutation Identification Pipeline
  • Overview
  • Features
  • Example Usage
  • Getting Started
• Installation
• Setup
  • Filename convention
  • Dependencies
• Adding a new program
  • Call DefineParameters
  • Command line arguments in GetOptions
  • if-block run checker in MAIN
  • Custom subroutine
  • Further information
• Structure
  • mip.pl
  • Sequence QC
  • Alignment
  • BAM file manipulation
  • Coverage QC
  • Variant calling
  • Variant QC
  • Variant Selection
  • Variant annotation
  • Variant evaluation
  • qcCollect.pl
  • covplots_exome.R / covplots_genome.R
• vcfParser
  • Usage
  • Installation
• QCCollect
  • Usage
  • Installation
  • SetUp
• score_mip_variants
  • Consequence
  • Frequency
  • Inheritance Model(s)
  • Protein Functional Prediction
  • Variant Quality Filter
  • Conservation
  • Combined Annotation Dependent Depletion (CADD)
  • ClinVar
• Dynamic Configuration File
• Pedigree File
  • On UPPMAX
  • Abbrevations
• Individual Identification Number (IDN)
  • IDN Definition
• The Code
  • Subroutines

Indices and tables

• Index
• Module Index
• Search Page