Table 4 Computation timea required with real sequence data for the longest (BTA1) and shortest (BTA29) chromosomes
From: Selecting sequence variants to improve genomic predictions for dairy cattle
Computational step | BTA1 | BTA29 |
|---|---|---|
Unzip VCF files | 6 | 2 |
Read and transpose sequence | 95 | 36 |
Subset sequenced animals | 1 | 1 |
Subset matching HD markers | 8 | 10 |
Merge sequence and HD data | 143 | 6 |
Compute sequence linkage | 3 | 1 |
Subset edited variants | 3 | 1 |
Fix Mendelian conflicts | 3 | 1 |
Impute with edited data | 16 | 10 |
Reduce some sequence to HD data | 1 | 1 |
Impute with reduced data | 17 | 9 |
Total | 296 | 78 |