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Table 2 Comparison of computational performance

From: ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole-genome sequencing data

Tool

Built-in parallelisation enabled?

Simulated samples (single-chromosome BAM files), minutes

Clinical samples (full BAM files), minutes

NA12878 (full BAM file), minutes

Joint calling, minutes

Manta

Auto

2.3(1.7)

76.5(21.0)

70

\(397^{\dagger }\)

CNVnator

Auto

1.4(0.7)

22.0(0.8)

32

\(133^{\dagger }\)

CNVpytor

Yes

3.6(2.1)

15.3(0.5)

27

\(121^{\dagger }\)

Control-FREEC

Yes

2.3(1.2)

31.2(7.2)

36

\(182^{\dagger }\)

ConanVarvar

Yes

1.7(0.9)

21.5(0.6)

32

63

ConanVarvar

No

1.8(0.8)

22.5(1.3)

33

131

  1. Mean and standard deviation (in brackets) of each tool’s execution time on different BAM files, calculated as the time it takes for a program to output the results of variant calling without running any additional scripts (e.g., for plots). An HPC server node with a total of 128 GB of RAM and 4 Intel Xeon CPUs was used in each run. Symbol \(^{\dagger}\) indicates that the value is an estimate