Using Mendelian error information for quality control
So, how can we infer the quality of calls using Mendelian inheritance rules? Let's look at expectations for different genotypical configurations of the parents:
- For a certain potential bi-allelic SNP, if the mother is AA and the father is also AA, then all offspring will be AA.
- If the mother is AA and the father TT, then all offspring will have to be heterozygous (AT). They always get an A from the mother and they always get a T from the father.
- If the mother is AA and the father is AT, then offspring can be either AA or AT. They always get the A from the mother, but they can get either an A or a T from the father.
- If the both the mother and the father are heterozygous (AT), then the offspring can be anything. In theory, there is not much we can do here.
In practice, we can ignore mutations, which is safe to do with most eukaryotes. The number of mutations (noise, from our perspective) is several orders of magnitude lower than the signal we...
