Allele calling using fitTetra

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fitTetra

fitTetra is an R package for genotype calling of tetraploid samples based on bi-allelic marker assays such as Illumina GoldenGate, Infinium and KASPar. The main characteristic of such assays is that they produce two signals for a sample for a given marker, one signal for each of the two alleles.

The functions in fitTetra take as input the ratios of these two signals, and fit a mixture model to the distribution of these ratios. The mixture model has five component distributions for the five possible tetraploid genotypes: nulliplex to quadruplex.

The main user function of the package, saveMarkerModels, iterates over all or a selected set of markers, fits a series of mixture models for each marker and selects the best model according to several criteria. Based on further criteria it then either rejects the marker, or it uses the selected model to assign genotype scores to each sample. Samples that cannot be genotyped reliably are assigned a missing value for the genotype. The output consists of a table with data on the fitted model per marker and a table with a.o. the assigned genotypes for each sample per marker. Optional further output includes a log file, a table with data on all fitted models per marker, and graphical output (e.g. Figure 1)

Figure 1. Typical graphical output of fitTetra. Upper panel: histogram of the signal ratios: allele a / (allele a + allele b) of a set of tetraploid potato varieties (white bars) and a diploid cross progeny (gray bars) for marker PotSNP016. The model fitted to the tetraploid varieties is indicated (green line). Lower panel: the genotype (0 to 4 for nulliplex to quadruplex) assigned to the tetraploid samples in relation to the signal ratios. Unassigned samples are shown at the bottom in red. The diploid samples coincide with the nulliplex, duplex and quadruplex peaks of the tetraploid samples.
Figure 1. Typical graphical output of fitTetra. Upper panel: histogram of the signal ratios: allele a / (allele a + allele b) of a set of tetraploid potato varieties (white bars) and a diploid cross progeny (gray bars) for marker PotSNP016. The model fitted to the tetraploid varieties is indicated (green line). Lower panel: the genotype (0 to 4 for nulliplex to quadruplex) assigned to the tetraploid samples in relation to the signal ratios. Unassigned samples are shown at the bottom in red. The diploid samples coincide with the nulliplex, duplex and quadruplex peaks of the tetraploid samples.

Detailed information on the use and output is given in the file fitTetra_Help.pdf. The operation of the package and an application are described in Voorrips et al (2011).

License

fitTetra is distributed free of charge under the GNU General Public License.

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