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Table 3 Comparison of homozygous 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 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
  1. 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.