Skip to main content

Table 1 Summary of the variants called by GATK and DeepVariant (DV)

From: The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle

Variant caller

Sets

Variants

SNPs

INDELs

Ti:Tv ratio

High impact predicted

SNPs / INDELs

GATK

Raw

18,654,649 (831,391)

16,135,130 (58,049)

2,617,546 (773,342)

2.16

2680 / 4493

GATK

Filtered-out

1,453,366 (239,008)

1,271,522 (8577)

279,871 (230,431)

1.66

428 / 500

GATK

Filtered

17,201,283 (592,383)

14,863,608 (49,472)

2,337,675 (542,911)

2.20

2252 / 3993

DV

Raw

18,748,114 (702,173)

16,554,438 (54,438)

2,401,933 (647,735)

2.24

3530 / 2778

DV

Filtered-out

1,571,454 (270,963)

1,174,815 (11,834)

393,927 (259,108)

2.19

1061 / 612

DV

Filtered

17,440,238 (577,997)

15,361,785 (42,899)

2,240,627 (535,098)

2.24

2474 / 2240

  1. Multiallelic sites are presented in parentheses. Ti:Tv ratios are restricted to biallelic SNPs. Functional consequences are predicted for biallelic SNPs / biallelic INDELs