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Table 2 Total number of single nucleotide variants (SNVs), insertions and deletions (InDels), and Transition/Transversion Ratios found using single and multi sample calling methods with HaplotypeCaller (HC), Platypus (PL), Platypus results after multi-nucleotide variants were split into allelic primitives (PL_PRIM), Samtools (SAM), and the UnifiedGenotyper (UG) for 65 animals

From: Evaluation of variant identification methods for whole genome sequencing data in dairy cattle

Calling method

Total number of SNVs

Total number of InDels

Transition/Transversion ratio

Single sample calling, combined

Multi sample calling

Single sample calling, combined

Multi sample calling

Single sample calling, combined

Multi sample calling

HC

-

19,901,885

-

2,685,032

-

2.138

PL

17,709,672

16,894,054

2,973,025

2,890,066

2.178

2.165

PL_PRIM

20,869,015

19,759,134

2,864,147

2,890,412

2.105

2.058

SAM

20,647,891

18,767,273

2,682,094

1,997,791

2.176

2.240

UG

21,984,283

22,048,382

2,485,677

2,741,468

2.024

1.974

  1. The combined results of all 65 single samples represent single sample calling results.