Welcome to Mendel,MD’s documentation!

Contents:

• Mendel,MD
• Requirements
• Other Libraries Needed
• OMIM Data
• Docker
• Manual Installation
• Installing PostgreSQL Database
• Installation on Ubuntu 16.04 LTS (tested)
• Installing Pynnotator
• Installing Mendel,MD
• Start the annotation
• Creating a superuser
• Importing Genes and Diseases Data
• Upload your VCFs using the web interface
• Deployment on RedHat/CentOS 7
• Pynnotator
• Libraries
• Databases
• Features
• Requirements
• Installation
• Test
• Clinical Cases
  • Upload of Examples
  • Autosomal Recessive - Homozygous
  • Autosomal Recessive - Compound Heterozygous
  • Autosomal Dominant - Heterozygous
  • Dominant X-linked - Hemizygous
• Filter Analysis
  • One Click
  • Family Analysis
  • Individuals Options
  • VCF Options
  • Annovar Options
• Description of the Fields
  • Func refGene
  • Gene.refGene
  • ExonicFunc.refGene
  • AAChange.refGene
  • phastConsElements46way
  • genomicSuperDups
  • esp6500si_all
  • 1000g2012apr_all
  • LJB2_SIFT
  • LJB2_PolyPhen2_HDIV
  • LJB2_PP2_HDIV_Pred
  • LJB2_PolyPhen2_HVAR
  • LJB2_PolyPhen2_HVAR_Pred
  • LJB2_LRT
  • LJB2_LRT_Pred
  • LJB2_MutationTaster
  • LJB2_MutationTaster_Pred
  • LJB_MutationAssessor
  • LJB_MutationAssessor_Pred
  • LJB2_FATHMM
  • LJB2_GERP++
  • LJB2_PhyloP
  • LJB2_SiPhy
  • cosmic65
  • avsift
  • SIFT
  • PolyPhen-2
  • Condel
• Extension

Indices and tables

• Index
• Module Index
• Search Page