SNPdat protocols

SNPdat specifications

Information


Unique identifier OMICS_00184
Name SNPdat
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


Add your version

Maintainer


  • person_outline Christopher J. Creevey <>

Publication for SNPdat

SNPdat IN pipelines

 (3)
2015
PMCID: 4607525
PMID: 26338191
DOI: 10.1093/gbe/evv168

[…] with the reference genome using mpileup command in samtools and variants were called with “bcftools.” snps obtained were then annotated on z. lateralis melanops genome using the perl script snpdat_v1.0.5.pl (doran and creevey 2013)., high-quality bird genomic data are rapidly accumulating (jarvis et al. 2014; zhang et al. 2014), allowing researchers to address a variety of questions […]

2015
PMCID: 4639833
PMID: 26553309
DOI: 10.1038/srep16358

[…] were aligned against the genome and annotation of european seabass (diclab1), nile tilapia (orenil1.1) and stickleback (gasterosterus aculeatus, broad v1.0) using the program gmap v13.8.1944 and snpdat v1.0.545 with default parameters. considering the divergence between asian seabass and each of the aforementioned three species, only loci with more than 70% of sequence length mapped […]

2014
PMCID: 4284805
PMID: 25534655
DOI: 10.1038/ncomms6770

[…] script to calculate the mean proportion of fixed differences per bp (df) between d. labrax and d. punctatus in 150-kb windows. snps were annotated to exonic, intronic or intergenic regions using snpdat67, and the mean expected heterozygosity in different regions was calculated with vcftools v0.1.11 (ref. 68)., variable recombination rates along each chromosome (ρ=4ner per kb) were estimated […]

SNPdat institution(s)
Teagasc Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Meath, Ireland

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