SNPdat protocols

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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


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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 ()., high-quality bird genomic data are rapidly accumulating (; ), allowing researchers to address a variety of questions regarding avian evolution that were problematic to tackle […]

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 v13.8.19 and snpdat v1.0.5 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 snpdat, and the mean expected heterozygosity in different regions was calculated with vcftools v0.1.11 (ref. )., variable recombination rates along each chromosome (ρ=4ner per kb) were estimated […]


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SNPdat in publications

 (9)
PMCID: 5601409
PMID: 28955357
DOI: 10.3389/fpls.2017.01565

[…] script implemented in the ksnp tool. the output is summarized in a variant call format file (vcf) file that was analyzed and filtered for those snps that are conserved only in the cv strains. snpdat software was used to annotate snps (). additional visual inspection of snps and analysis of amino acid conservation in selected cluster of orthologs was conducted using jalview alignment tool […]

PMCID: 5367300
PMID: 28386436
DOI: 10.1098/rsos.160805

[…] to those obtained when not taking the transmission mode into account. to assess whether any associated snp might lead to changes in protein sequence, we performed an annotation using the software snpdat (v. 1.0.5) [] and using gene coordinates from []., to determine when and on which specific allele selection occurred, we used the coalescent framework implemented in argweaver []. argweaver […]

PMCID: 5364355
PMID: 28085156
DOI: 10.1038/ismej.2016.172

[…] (), version 2.1.8. with the unifiedgenotyper tool (options: -dcov 50 for 4 × coverage alignment). the resulting vcf files were analysed to identify for each snp whether it was synonymous using snpdat version 1.0.4 (). all vcf files were then combined for analysis using the combinevariants command of gatk (options: -genotypemergeoptions uniquify to make all sample genotypes unique by file […]

PMCID: 5726852
PMID: 29231813
DOI: 10.7554/eLife.30925.041

[…] reads from strain d188-5 to the d188 reference genome sequence. variants (snps) were called using freebayes, filtered to those with quality score greater than 20 using vcffilter, and annotated using snpdat v. 1.0.5 ()., seedling root inhibition assays were performed as described previously, with the exception that after bacteria were adjusted to od600 = 0.5, they were sometimes diluted […]

PMCID: 4909269
PMID: 27304978
DOI: 10.1371/journal.pgen.1006111

[…] assessed using bedtools v2.17.0 []. single nucleotide variants (snvs) and their proportion among all reads were called using lofreq* v2.1.1 [] and their effect at the amino-acid level assessed by snpdat v.1.0.5 []., two sets of snv markers were used for analyses of genetic diversity and natural selection. the ‘full’ marker set excluded all nucleotide positions in a given sample that had (i) […]


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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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