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Depositordc.contributorWard, Paulineen
Funderdc.contributor.otherBBSRC - Biotechnology and Biological Sciences Research Councilen_UK
Data Creatordc.creatorPrendergast, Jamesen_UK
Data Creatordc.creatorMaclean, Colin A.en_UK
Data Creatordc.creatorChue Hong, Neilen_UK
Date Accessioneddc.date.accessioned2015-02-11T16:57:30Z
Date Availabledc.date.available2015-02-11T16:57:30Z
Citationdc.identifier.citationPrendergast, James; Maclean, Colin A.; Chue Hong, Neil. (2015). hapbin: An efficient program for performing haplotype based scans for positive selection in large genomic datasets, [Dataset]. University of Edinburgh. Roslin Institute. https://doi.org/10.7488/ds/214.en
Persistent Identifierdc.identifier.urihttps://hdl.handle.net/10283/714
Persistent Identifierdc.identifier.urihttps://doi.org/10.7488/ds/214
Dataset Description (abstract)dc.description.abstractThese files contain genome-wide integrated haplotype scores (iHS) for each of the 26 populations in the phase 3 release of the 1000 genomes project. iHS were calculated using the hapbin program that can be downloaded from https://github.com/evotools/hapbin. The 1000 genomes phased haplotypes were obtained from mathgen.stats.ox.ac.uk/impute and hapbin was run with default parameters. The iHS are provided in two formats; BED and bedGraph. For each SNP the unstandardised iHS was calculated as ln(iHH1/iHH0) and these values normalised using hapbin’s default parameters. If the normalised iHS was negative the absolute value is reported and this is indicated by a 1 in the fourth column following the “:” of the BED format file. The bedGraph formatted data can be easily viewed along the genome at the UCSC genome browser by specifying the URL to the corresponding file at http://genome-euro.ucsc.edu/cgi-bin/hgCustom?clade=mammal&org=Human&db=hg37.en_UK
Dataset Description (TOC)dc.description.tableofcontentsThe following files are available for download here: (a) Documentation relating to methods ("fileDescriptions.txt"/"fileDescriptions.pdf"); (b) 572 files in bedGraph format (.bg.gz), covering different chromosomes and different populations from the 1000 Genomes project. These may be extracted using gunzip (on Linux/UNIX) or for example 7-Zip on Windows. (c) One tar (tape archive) file containing 572 files in BED format, similarly covering different chromosomes and populations. These may be untarred using the tar program (on Linux/UNIX) or for example 7-Zip on Windows.en_UK
Publisherdc.publisherUniversity of Edinburgh. Roslin Instituteen_UK
Relation (Is Referenced By)dc.relation.isreferencedbyMol Biol Evol (2015) doi: 10.1093/molbev/msv172 http://mbe.oxfordjournals.org/content/early/2015/08/05/molbev.msv172.abstract?keytype=ref%2520&ijkey=NyuY69Xrzb1HqV3en_UK
Relation (Is Referenced By)dc.relation.isreferencedbyhttps://github.com/evotools/hapbinen_UK
Sourcedc.sourcehttps://mathgen.stats.ox.ac.uk/impute/1000GP%20Phase%203%20haplotypes%206%20October%202014.htmlen_UK
Sourcedc.sourcehttp://genome.ucsc.edu/FAQ/FAQformat.html#format1en_UK
Sourcedc.sourcehttp://genome.ucsc.edu/FAQ/FAQformat.html#format1.8en_UK
Subjectdc.subjectHomo sapiens
Subjectdc.subjectgenomics
Subject Classificationdc.subject.classificationBiological Sciences::Genetics
Titledc.titlehapbin: An efficient program for performing haplotype based scans for positive selection in large genomic datasetsen_UK
Typedc.typedataseten_UK

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