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Table 2 Comparison of heterozygous SNP calls made from BovineHD BeadChip genotype data and the resequencing pipelines.

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

Pipeline

Consistent

Heterozygous > homozygous

As indel

Inconsistent

BWA + SAMtools

167,758 (93.8%)

10,590 (5.9%)

30

477

CLC Genomics Workbench

175,322 (94.6%)

9,589 (5.2%)

46

438

Mosaik + GigaBayes

158, 564 (97.1%)

4,467 (2.7%)

196

0

SMALT + SAMtools

151,792 (94.1%)

9,097 (5.6%)

31

401

  1. Consistent, the same alleles at the same sites were determined by both the chip and resequencing methods; Heterozygous > homozygous, heterozygotes called on the chip were under-called as homozygote with one identical allele in the resequencing pipelines; As indels, SNP sites on the chip were called as indels in resequencing pipelines; Inconsistent, heterozygous calls with the chip and resequencing pipelines but with different alleles.
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BMC Genomics

ISSN: 1471-2164

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