Codes in Harmonised Sumstats
hm_coordinate_conversion
| Value | Description of the genome mapping process |
|---|---|
| rs | Update base pair location value by mapping rsID using reference |
| lo | liftover base pair location to the target genome build (GRCh 38) |
hm_code
| Code | Description of Harmonisation Process |
|---|---|
| 1 | Palindromic; Infer strand; Forward strand; Alleles correct |
| 2 | Palindromic; Infer strand; Forward strand; Flipped alleles |
| 3 | Palindromic; Infer strand; Reverse strand; Alleles correct |
| 4 | Palindromic; Infer strand; Reverse strand; Flipped alleles |
| 5 | Palindromic; Assume forward strand; Alleles correct |
| 6 | Palindromic; Assume forward strand; Flipped alleles |
| 7 | Palindromic; Assume reverse strand; Alleles correct |
| 8 | Palindromic; Assume reverse strand; Flipped alleles |
| 9 | Palindromic; Drop palindromic; Not harmonised |
| 10 | Forward strand; Alleles correct |
| 11 | Forward strand; Flipped alleles |
| 12 | Reverse strand; Alleles correct |
| 13 | Reverse strand; Flipped alleles |
| 14 | Required fields are not known; Not harmonised |
| 15 | No matching variants in reference VCF; Not harmonised |
| 16 | Multiple matching variants in reference VCF; Not harmonised |
| 17 | Palindromic; Infer strand; EAF or reference VCF AF not known; Not harmonised |
| 18 | Palindromic; Infer strand; EAF < specified minor allele frequency threshold; Not harmonised |