Table 1 Comparison of GBS data analysis using UNEAK vs. Haplotag software
SoftwareModeTime (hr:min)Number of Loci Passing Population Filter at Indicated Genotype CompletenessSNP Loci (80%) Duplicated by Alternate Pipeline
Haplotype LociSNP loci
50%80%50%80%NumberPercent
UNEAKNA6:05NANA12,7804,2604204a99%a
HaplotagCluster discovery6:54b29,42111,95043,37817,1174108c24%c
HaplotagProduction0:11b24,412734331,6858872NANA
  • a Number and percent of SNP-based loci called by UNEAK that were duplicated by Haplotag at the same 80% filtering level.

  • b Times for Haplotag runs do not include the 6 hr required for generation of tag-count files using UNEAK.

  • c Number and percent of SNP-based loci called by Haplotag that were duplicated by UNEAK at the same 80% filtering level.