Pedigree summary
This table shows the pedigree TSV file that was input to the workflow
- Sex - (1=male; 2=female; other=unknown)
- Phenotype - (-9=missing;0=missing;1=unaffected;2=affected).
| Family ID | Individual ID | Paternal ID | Maternal ID | Sex | Phenotype |
|---|---|---|---|---|---|
| Ashkenazi | hg002 | hg003 | hg004 | 1 | 1 |
| Ashkenazi | hg003 | 0 | 0 | 1 | 1 |
| Ashkenazi | hg004 | 0 | 0 | 2 | 1 |
Mendelian conflict summary
This table provides stats from the RTG Mendelian Report
Find more information about the RTG Mendelian tool here.These are the definitions of the columns you will find in the table.
- Family: Family ID.
- Total records: Total number of records in the VCF.
- Total variants: Total number of variants identified in the multi-sample VCF that were variant in at least 1 family member.
- Percent variant: Percentage of the VCF that is variant in at least 1 family member.
- Concordance M: Percentage of variants that are in concordance with the Male.
- Concordance F: Percentage of variants that are in concordance with the Female.
- Concordance M+F: Percentage of variants that are in concordance with both the Male and Female.
- Unexpected ploidy: Percentage of records that did not conform to expected ploidy.
- Incomplete calls: Percentage of records that had indeterminate consistency status due to incomplete calls.
- Total conflicts: Number of records that contained a violation of Mendelian constraints.
- Percentage conflict: Percentage of records that contained a violation of Mendelian constraints.
| Family | Total records | Total variants | Perc variant | Concordance M | Concordance F | Concordance M+F | Unexpected ploidy | Incomplete calls | Total conflicts | Perc conflict |
|---|---|---|---|---|---|---|---|---|---|---|
| Ashkenazi | 53 | 49 | 92.45% | 91.11% | 88.89% | 79.55% | 0.00% | 8.16% | 10 | 20.41% |