Roslin Bioinformatics - Genotype Checker

Loading Data

Paired Pedigree and Genotype data files are loaded via the 'Load Pedigree' followed by 'Load Genotype' buttons.
On loading the Pedigree the data is displayed in tabular form (in the 'Pedigree' tab), and a message is reported in the 'Messages' tab. This message will report any problems loading the data, such as any input lines ignored because of format errors or any Individuals ignored through Pedigree inconsistencies (e.g. inconsistent sex, a male being used as a dam etc). When the Genotype File is loaded the file is parsed and checked for validity, and a 'Markers' display generated, where the user can select markers to analyse (see Inheritance Checking).

File Format

Data is loaded as separate Pedigree and Genotype files.

Pedigree File Format

ma1[SPACE] 0[SPACE] 0[SPACE] F[CR]
pa1 0 0 M
bob pa1 ma1 M
bill pa1 ma1 M
ma2 0 0 F
jill pa1 ma1 F
gus pa1 ma2 M

notes

  • Each line represents   individualID  sireID  damID  sex(M/F/U)
  • All four values are required (lines without four or five values are ignored)
  • Values are separated by white space
  • Individuals should have unique names (with no spaces)
  • unknown parentIDs must be recorded as '0' (zero)
  • An optional fifth column can be added with a litterID (with no spaces)
  • various pedigree inconsistencies (e.g. female sires) will be detected and reported,
    and require fixing before the pedigree can be used

Genotype File Format

ma1[SPACE] IQ[SPACE] A[SPACE] A[CR]
pa1 IQ D D
bob IQ A D
bill IQ A ?
ma1 eyes 2 2
pa1 eyes 3
bob eyes 2 3
bill eyes ?
ma1 sexL B B
pa1 sexL A Y-null
bob sexL ?
bill sexL Y-null ?
bill sexL Y-null

notes

  • Each line represents:   individualID  MarkerID  allele1  allele2
  • Lines with fewer than 3 values are ignored (as there is no Genotype information presented)
  • Values are separated by white space
  • There is no significance in the order of alleles
  • '?' indicates allele value unknown
  • A single allele value is interpreted as homozygous
  • Sex-linked Genotypes should have a null marker (e.g. 'Y-null')
    asserted in the heterogametic individuals,
    and care taken not to assert homozygosity for this
    (i.e. the last line above is wrong).