Allowed Configuration Values

This is a reference list of allowed values for various configuration variables and attributes.

Booleans

  • yes
  • Yes
  • true
  • True
  • no
  • No
  • false
  • False

Gene effect types

  • 3'UTR
  • 3'UTR-intron
  • 5'UTR
  • 5'UTR-intron
  • frame-shift
  • intergenic
  • intron
  • missense
  • no-frame-shift
  • no-frame-shift-newStop
  • noEnd
  • noStart
  • non-coding
  • non-coding-intron
  • nonsense
  • splice-site
  • synonymous
  • CDS
  • CNV+
  • CNV-

Gene effect groups

This lists the valid gene effect groups and which effect types they encompass.

  • Coding
    • Nonsense
    • Frame-shift
    • Splice-site
    • No-frame-shift-newStop
    • Missense
    • No-frame-shift
    • noStart
    • noEnd
    • Synonymous
  • Noncoding
    • Non coding
    • Intron
    • Intergenic
    • 3'-UTR
    • 5'-UTR
  • CNV
    • CNV+
    • CNV
  • LGDs
    • Frame-shift
    • Nonsense
    • Splice-site
    • No-frame-shift-newStop
  • Nonsynonymous
    • Nonsense
    • Frame-shift
    • Splice-site
    • No-frame-shift-newStop
    • Missense
    • No-frame-shift
    • noStart
    • noEnd
  • UTRs
    • 3'-UTR
    • 5'-UTR

Sex

  • 0 or U or unspecified
  • 1 or M or male
  • 2 or F or female

Inheritance

  • reference
  • mendelian
  • denovo
  • possible_denovo
  • omission
  • other
  • missing
  • unknown

Role

  • maternal_grandmother
  • maternal_grandfather
  • paternal_grandmother
  • paternal_grandfather
  • mom
  • dad
  • parent
  • prb
  • sib
  • child
  • maternal_half_sibling
  • paternal_half_sibling
  • half_sibling
  • maternal_aunt
  • maternal_uncle
  • paternal_aunt
  • paternal_uncle
  • maternal_cousin
  • paternal_cousin
  • step_mom
  • step_dad
  • spouse
  • unknown

Status

Unspecified values indicate unknown status.

  • 0: unknown
  • 1: unaffected
  • 2: affected

VariantType

  • sub or substitution
  • ins or insertion
  • del or deletion
  • complex
  • CNV