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