FastTagger

[…] ction of genomic haplotypes in the 485 horses both within and across breeds. Tagging SNPs that reconstructed haplotypes across all 485 horses (inter-breed tag SNPs) were identified using the software FastTagger []. In total, 355,903 tagging SNPs were needed to reconstruct haplotypes present across all the horses in the cohort with a minor allele frequency (MAF) > 0.01 and tag-SNP r2 > 0.99. These […]

[…] are []. Furthermore, there are many other methods have been recently proposed, including the weighted tag-SNP-set analytical method [], the CLONTagger method [], the diSNP selection method [] and the FastTagger method []. Meanwhile, it is inevitable to yield very noisy covariance matrices and face multiple testing problems once extending the proposed statistic to a large genome-wide scale, which s […]

[…] ic strengths of the recombination hotspot located inside the 100-SNP window. For each hotspot, a profile of the estimated recombination strengths will be output. For the genotype data, we applied the FastTagger [] tool to select all tag SNPs with MAF higher than 0.3 from the HapMap Phase 3 data of JPT+CHB population. The minimal r2 was set to 0.9. As such we obtained 179,671 tag SNPs. The Python s […]

[…] lled tag SNPs that are subsets sufficient to infer the other SNPs from. Common methods suffer from various problems with larger chromosomes, thus becoming very memory-intensive and time-consuming []. FastTagger [] incorporated frequent itemset mining to overcome several of these problems. […]