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FastTagger specifications

Information


Unique identifier OMICS_19868
Name FastTagger
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Guimei Liu

Publication for FastTagger

FastTagger citations

 (4)
library_books

Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

2017
BMC Genomics
PMCID: 5530493
PMID: 28750625
DOI: 10.1186/s12864-017-3943-8

[…] 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 […]

library_books

A powerful score based test statistic for detecting gene gene co association

2016
BMC Genet
PMCID: 4731962
PMID: 26822525
DOI: 10.1186/s12863-016-0331-3

[…] 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 […]

call_split

ARG walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis

2015
BMC Genomics
PMCID: 4682399
PMID: 26679564
DOI: 10.1186/1471-2164-16-S12-S1
call_split See protocol

[…] 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 […]

library_books

A primer to frequent itemset mining for bioinformatics

2013
Brief Bioinform
PMCID: 4364064
PMID: 24162173
DOI: 10.1093/bib/bbt074

[…] 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. […]

Citations

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FastTagger institution(s)
Department of Computer Science, National University of Singapore, Singapore; NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
FastTagger funding source(s)
Supported in part by an A*STAR grant SERC 072 101 0016 and an NUS NGS scholarship.

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