Table 1 Results for ConSTRain, GangSTR, and HipSTR on the HG002 human benchmark

From: Genotyping short tandem repeats across copy number alterations, aneuploidies, and polyploid organisms

   

Memory usage (MB)

Unfiltered

Filtered

Method

Runtime (hrs)

Throughput (loci/s)

Base

Per addtnl. thread

Loci called (%)

Accuracy

Loci called (%)

Accuracy

ConSTRaina

0.33

1480.48

33.95

15.28

1655655 (97.63)

0.9525

1393426 (82.17)

0.9828

GangSTR

14.91

32.31

31.44

NA

1654569 (97.56)

0.9513

1372842 (80.95)

0.9769

HipSTR

11.99

40.15

401.89

NA

1225530 (72.27)

0.9750

1174890 (69.28)

0.9774

  1. Data are shown before and after filtering the output of each tool. The total number of loci in the benchmark was 1695865. The percentage of this number that was called by each variant caller is shown in brackets in the ’Loci called’ columns. Memory usage statistics are based on the ’Maximum resident set size’ reported when running each tool under the GNU time command with the –verbose flag. The best value in each column is printed in bold.
  2. aData for ConSTRain running on 32 threads are shown. Single-threaded runtime was 6.73 h (71.50 loci/s).
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