Table 1 Comparison of variant counts for the 6 pipelines with HG002 sequenced 70 times in different runs. Displayed are means and standard deviations (in parenthesis).

From: Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment

Mapping/alignment

Variant calling

DRAGEN-DRAGEN

DRAGEN-DeepVariant

DRAGEN-GATK

GATK-DRAGEN

GATK-DeepVariant

GATK-GATK

Failed filters

58,072 (1290)

2,464,646 (195,004)

64,495 (1374)

78,883 (2164)

1,992,543 (116,083)

47,017 (1075)

Passed filters

5,066,013 (3669)

4,839,100 (2611)

4,826,743 (5615)

4,840,437 (7688)

4,679,657 (3452)

4,772,371 (9821)

SNVs

4,080,672 (2417)

3,914,177 (1177)

3,889,807 (3161)

3,849,055 (3745)

3,789,168 (1608)

3,860,497 (5909)

Insertions

478,685 (996)

444,619 (1122)

447,413 (1662)

441,575 (1876)

425,348 (1658)

434,662 (2302)

Deletions

481,852 (603)

455,649 (650)

450,115 (972)

440,488 (1451)

441,116 (998)

439,814 (1735)

Complex variants

24,803 (198)

24,097 (162)

21,378 (334)

22,476 (454)

23,352 (194)

20,547 (439)

Ti/Tv

1.960 (0.00116)

1.998 (0.00073)

1.960 (0.00152)

1.997 (0.00194)

1.992 (0.00074)

1.971 (0.00217)

  1. Target sensitivities of 99.95% for SNVs and 99.75% for Indels were used for pipelines involving the GATK Haplotypecaller. SNV single nucleotide variation, Ti/Tv transition/transversion.
Back to article page