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Table 1 SNPs called on the UMD3.1 assembly using different pipelines.

From: Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

Tools

Algorithm

SNPs

Homozygous

Heterozygous

BWA + SAMtools

Bayesian *

4,434,826

2,164,136

2,270,690

CLC Genomics Workbench

NQS

4,740,179

1,997,225

2,742,954

SMALT + SAMtools

Bayesian *

4,077,556

2,144,671

1,932,885

Mosaik + GigaBayes

Bayesian

3,993,407

1,732,242

2,261,165

  1. NQS, Neighbourhood Quality Standard; * pipelines that were implemented with mapping quality.
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BMC Genomics

ISSN: 1471-2164

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