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

Table 3 Comparison of homozygous SNP calls made from BovineHD BeadChip genotype data and the resequencing pipelines.

Pipeline	Consistent	Homozygous > heterozygous	As indel	Inconsistent
BWA + SAMtools	253,102 (99.9%)	247 (0.1%)	107	16
CLC Genomics Workbench	254,195 (99.6%)	848 (0.3%)	101	28
Mosaik + GigaBayes	236,261 (97.8%)	3,522 (1.4%)	1,860 (0.8%)	20
SMALT + SAMtools	247,805 (99.8%)	272 (0.1%)	96	19

Consistent, the same alleles at the same sites were determined by both the chip and resequencing methods; Homozygous > heterozygous, homozygous SNPs called on the chip that were over-called as heterozygous in the resequencing pipelines; As indels, SNP sites on the BovineHD BeadChip that were called as indels in resequencing pipelines; Inconsistent, homozygous calls with both the BovineHD BeadChip and the resequencing pipelines but with different alleles.