Overview

This documentation covers the sources of annotation used in CGAP for genes and variants. It also provides information on the creation of custom reference files used in the CGAP Pipelines.

Copies of the files referred to in these docs are stored in the S3 bucket:

s3://cgap-annotations

The bucket is private and not meant for public files sharing. It is intended for internal back-up only and most of the files are stored in deeper archive tiers.

• Gene Annotations
  • Data Sources
    • RefSeq
      • Files
      • Description
      • Version
• Variant Annotations
  • Data Sources
    • VEP
      • Annotation Sources
      • Run VEP
    • dbSNP
    • Cytoband
    • HGVSg
    • Version
• Other References
  • hg38/GRCh38 Genome Build
  • HaplotypeCaller Exome Region File
    • VEP v101
    • Reference File Creation
  • BICseq2 Mappability File
  • Unrelated Files and Panel of Normal
    • SNV Pipeline - Unrelated RCK files
      • Sentieon
      • GATK
    • Somatic Sentieon - Panel of Normal (PON)
    • SV Pipeline - Manta
    • CNV Pipeline - BICseq2
  • ASCAT Resources
    • Loci Files
    • Allele Files
    • GC Correction File
  • Lift-over Chain Files
    • hg19/GRCh37 to hg38/GRCh38
    • hg38/GRCh38 to hg19/GRCh37