Table 4. Recommended software for each step of the genetic marker data curation workflow when using Illumina Infinium SNP arrays.
| Workflow step | Recommended software |
|---|---|
| Identify polyploids, aneuploids, and samples with low quality | GenomeStudio to obtain B-allele frequencies, |
| R to plot B-allele frequency for each sample | |
| Create subset of reliable SNPs | ASSIsT |
| Identify duplicate samples | PLINK |
| Identify incorrect P(P)C relationships | GenomeStudio |
| Identify unknown P(P)C relationships | R |
| Identify unknown grandparent-grandchild relationships | Excel* |
| Identify and resolve (remaining) Mendelian-inconsistent errors | GenomeStudio, FlexQTL |
| Identify and resolve Mendelian-consistent errors | Visual FlexQTL + GenomeStudio |
| Identify and correct map order inconsistencies | Visual FlexQTL |
| Identify phasing issues | FlexQTL + Visual FlexQTL |
| Haploblock border determination | Visual FlexQTL |
| Haplotype determination | |
| - Phasing | FlexQTL |
| - Haplotype assignment | PediHaplotyper |
| - Curation (automated) | FlexQTL |
* Template in Suppl. File 1 of Van de Weg and co-workers (2018) [23]