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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
  1. aTime in minutes