Table 1. Errors observed during the curation process and their possible causes.
Causes that should be (mostly) already resolved by the stage a researcher would start checking for specific errors are in parentheses and italicized.
| Error | Cause | Solution |
|---|---|---|
| Low call rate and impossible cluster identification | Probe binding issues | Remove SNP from data set |
| Unexpected B-allele frequencies | (Probe binding issues) | (Remove SNP from data set) |
| Unexpected ploidy | Remove sample from data set | |
| Low sample quality | Remove sample from data set | |
| High number P(P)C errors | (Probe binding issues) | (Remove SNP from data set) |
| (Low sample quality) | (Remove sample from data set) | |
| Incorrect pedigree | Adjust pedigree record | |
| Incorrect clustering | Manually determine genotype clusters | |
| Incorrect genotype call(s) not due to cluster issues | Adjust genotype call(s) or remove SNP from data set | |
| Low number P(P)C errors | (Probe binding issues) | (Remove SNP from data set) |
| (Low sample quality) | (Remove sample from data set) | |
| (Incorrect pedigree) | (Adjust pedigree record) | |
| Incorrect clustering | Manually determine genotype clusters | |
| Incorrect genotype call(s) not due to cluster issues | Adjust genotype call(s) | |
| High number double recombinations | (Probe binding issues) | (Remove SNP from data set) |
| (Low sample quality) | (Remove sample from data set) | |
| (Incorrect pedigree) | (Adjust pedigree record) | |
| (Unexpected ploidy) | (Remove sample from data set) | |
| Incorrect clustering | Manually determine genotype clusters | |
| Incorrect marker position in map | Adjust marker position or remove marker if it cannot be accurately mapped | |
| Incorrect genotype call(s) not due to cluster issues | Adjust genotype call(s) | |
| Incorrect phasing | Find responsible individual and make genotype missing | |
| Low number double recombinations | (Probe binding issues) | (Remove SNP from data set) |
| (Low sample quality) | (Remove sample from data set) | |
| (Incorrect pedigree) | (Adjust pedigree record) | |
| (Incorrect clustering) | (Manually determine genotype clusters) | |
| Nearby double recombination* | Resolve nearby double recombination | |
| Incorrect marker position in map | Adjust marker position or remove marker if it cannot be accurately mapped | |
| Incorrect genotype call(s) not due to cluster issues | Adjust genotype call(s) | |
| Incorrect phasing | Wait for haploblock analysis to resolve issue | |
| Incorrect haplotype determination | (Probe binding issues) | (Remove SNP from data set) |
| (Low sample quality) | (Remove sample from data set) | |
| (Incorrect pedigree) | (Adjust pedigree record) | |
| (Incorrect clustering) | (Manually determine genotype clusters) | |
| (Incorrect marker position in map) | (Adjust marker position or remove marker if it cannot be accurately mapped) | |
| (Incorrect genotype call(s) not due to cluster issues) | (Adjust genotype call(s)) | |
| Incorrect phasing | Manually correct phasing (determine correct haplotypes) | |
| Recombination within haplotype | Adjust haploblock borders |
*Nearby double recombination can occur for two adjacent markers with many double recombinations and markers with few double recombinations. However, nearby double recombinations rarely lead to a high number of double recombinations for a single marker