...
Consensus calling is currently only available using the algorithm ‘majority genotype (favoring homozygotes)’. This means that only parent replicate samples are consensus called. The parent samples are identified by the fields germplasm_par1 and germplasm_par2 which reference the germplasm_name of the parents
The term ‘favoring homozygotes' means that if there are equal frequencies of homozygous and heterozygous genotype calls, then the homozygous genotype is consensus called. For example: if there are replicate samples AA AA AT and AT, then the consensus call will be AA. However, if there are equal frequencies of homozygous calls, eg replicate samples AA AA TT and TT, then the consensus call will be NN or missing, as there is an equal tie between two different homozygous calls. Equal frequencies of homozygous calls will take precedence, so that if replicate samples are AA, AT and TT, the consensus call will be NN.
A consensus threshold can be optionally applied if more stringency in the consensus calling is needed, e.g. if the user wants at least 50% of one call to be observed. For example, if the replicate samples are AA AA AT AT TT, and a 50% consensus threshold is applied, then the consensus call will be an NN, as less than 50% of the calls are AA. However, AA AA AA AT and TT will return a consensus call of AA as now more than 50% of the calls are AA
Select ‘APPLY’. A preview of the consensus calling can be viewed in the screen. Each consensus called parent can be selected from the drop-down menu to see the contributing replicate sample calls. The consensus calls can be edited if the user does not agree with the calls.
To see all the consensus calls, click on ‘Download’ to view the consensus calling in Excel
...