Table 4

Categories of genotype permutations explored in VIPER.

Category

Permutation


1.

Copy (one-way) complete genotypes between individuals

2.

Copy (one-way) some genotypes between individuals

3.

Swap all genotypes from one into a different individual

4.

Swap some genotypes from one into a different individual

5.

Mix some random genotypes into individual

6.

Regenotyped family with novel father

7.

Regenotyped litter with novel father

8.

Regenotyped full sire sib set with novel father

9.

Regenotyped individual with novel father

10.

Score sex linked marker as homozygous

11.

Swap non sibling IDs between generations

12.

Swap non sibling IDs in same generation

13.

Swap sire sibling IDs in same generation

14.

Swap siblings IDs


All permutations (1-14) apart from No.7 were readily identified in the sandwich overview visualisation. Although offspring can be sorted by litter information, there is as yet no suitable visualisation for litter mates; consequently attention is not drawn to errors restricted to a particular litter.

Paterson et al. BMC Bioinformatics 2012 13(Suppl 8):S5   doi:10.1186/1471-2105-13-S8-S5

Open Data