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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.