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<html>
<title>PLINK</title>
<body>
<head>
<link rel="stylesheet" href="plink.css" type="text/css">
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=utf-8">
<title>PLINK: Whole genome data analysis toolset</title>
</head>
<!--<html>-->
<!--<title>PLINK</title>-->
<!--<body>-->
<font size="6" color="darkgreen"><b>plink...</b></font>
<div style="position:absolute;right:10px;top:10px;font-size:
75%"><em>Last original <tt>PLINK</tt> release is <b>v1.07</b>
(10-Oct-2009); <b>PLINK 1.9</b> is now <a href="plink2.shtml"> available</a> for beta-testing</em></div>
<h1>Whole genome association analysis toolset</h1>
<font size="1" color="darkgreen">
<em>
<a href="index.shtml">Introduction</a> |
<a href="contact.shtml">Basics</a> |
<a href="download.shtml">Download</a> |
<a href="reference.shtml">Reference</a> |
<a href="data.shtml">Formats</a> |
<a href="dataman.shtml">Data management</a> |
<a href="summary.shtml">Summary stats</a> |
<a href="thresh.shtml">Filters</a> |
<a href="strat.shtml">Stratification</a> |
<a href="ibdibs.shtml">IBS/IBD</a> |
<a href="anal.shtml">Association</a> |
<a href="fanal.shtml">Family-based</a> |
<a href="perm.shtml">Permutation</a> |
<a href="ld.shtml">LD calcualtions</a> |
<a href="haplo.shtml">Haplotypes</a> |
<a href="whap.shtml">Conditional tests</a> |
<a href="proxy.shtml">Proxy association</a> |
<a href="pimputation.shtml">Imputation</a> |
<a href="dosage.shtml">Dosage data</a> |
<a href="metaanal.shtml">Meta-analysis</a> |
<a href="annot.shtml">Result annotation</a> |
<a href="clump.shtml">Clumping</a> |
<a href="grep.shtml">Gene Report</a> |
<a href="epi.shtml">Epistasis</a> |
<a href="cnv.shtml">Rare CNVs</a> |
<a href="gvar.shtml">Common CNPs</a> |
<a href="rfunc.shtml">R-plugins</a> |
<a href="psnp.shtml">SNP annotation</a> |
<a href="simulate.shtml">Simulation</a> |
<a href="profile.shtml">Profiles</a> |
<a href="ids.shtml">ID helper</a> |
<a href="res.shtml">Resources</a> |
<a href="flow.shtml">Flow chart</a> |
<a href="misc.shtml">Misc.</a> |
<a href="faq.shtml">FAQ</a> |
<a href="gplink.shtml">gPLINK</a>
</em></font>
</p>
<table border=0>
<tr>
<td bgcolor="lightblue" valign="top" width=20%>
<font size="1">
<a href="index.shtml">1. Introduction</a> </p>
<a href="contact.shtml">2. Basic information</a> </p>
<ul>
<li> <a href="contact.shtml#cite">Citing PLINK</a>
<li> <a href="contact.shtml#probs">Reporting problems</a>
<li> <a href="news.shtml">What's new?</a>
<li> <a href="pdf.shtml">PDF documentation</a>
</ul>
<a href="download.shtml">3. Download and general notes</a> </p>
<ul>
<li> <a href="download.shtml#download">Stable download</a>
<li> <a href="download.shtml#latest">Development code</a>
<li> <a href="download.shtml#general">General notes</a>
<li> <a href="download.shtml#msdos">MS-DOS notes</a>
<li> <a href="download.shtml#nix">Unix/Linux notes</a>
<li> <a href="download.shtml#compilation">Compilation</a>
<li> <a href="download.shtml#input">Using the command line</a>
<li> <a href="download.shtml#output">Viewing output files</a>
<li> <a href="changelog.shtml">Version history</a>
</ul>
<a href="reference.shtml">4. Command reference table</a> </p>
<ul>
<li> <a href="reference.shtml#options">List of options</a>
<li> <a href="reference.shtml#output">List of output files</a>
<li> <a href="newfeat.shtml">Under development</a>
</ul>
<a href="data.shtml">5. Basic usage/data formats</a>
<ul>
<li> <a href="data.shtml#plink">Running PLINK</a>
<li> <a href="data.shtml#ped">PED files</a>
<li> <a href="data.shtml#map">MAP files</a>
<li> <a href="data.shtml#tr">Transposed filesets</a>
<li> <a href="data.shtml#long">Long-format filesets</a>
<li> <a href="data.shtml#bed">Binary PED files</a>
<li> <a href="data.shtml#pheno">Alternate phenotypes</a>
<li> <a href="data.shtml#covar">Covariate files</a>
<li> <a href="data.shtml#clst">Cluster files</a>
<li> <a href="data.shtml#sets">Set files</a>
</ul>
<a href="dataman.shtml">6. Data management</a> </p>
<ul>
<li> <a href="dataman.shtml#recode">Recode</a>
<li> <a href="dataman.shtml#recode">Reorder</a>
<li> <a href="dataman.shtml#snplist">Write SNP list</a>
<li> <a href="dataman.shtml#updatemap">Update SNP map</a>
<li> <a href="dataman.shtml#updateallele">Update allele information</a>
<li> <a href="dataman.shtml#refallele">Force reference allele</a>
<li> <a href="dataman.shtml#updatefam">Update individuals</a>
<li> <a href="dataman.shtml#wrtcov">Write covariate files</a>
<li> <a href="dataman.shtml#wrtclst">Write cluster files</a>
<li> <a href="dataman.shtml#flip">Flip strand</a>
<li> <a href="dataman.shtml#flipscan">Scan for strand problem</a>
<li> <a href="dataman.shtml#merge">Merge two files</a>
<li> <a href="dataman.shtml#mergelist">Merge multiple files</a>
<li> <a href="dataman.shtml#extract">Extract SNPs</a>
<li> <a href="dataman.shtml#exclude">Remove SNPs</a>
<li> <a href="dataman.shtml#zero">Zero out sets of genotypes</a>
<li> <a href="dataman.shtml#keep">Extract Individuals</a>
<li> <a href="dataman.shtml#remove">Remove Individuals</a>
<li> <a href="dataman.shtml#filter">Filter Individuals</a>
<li> <a href="dataman.shtml#attrib">Attribute filters</a>
<li> <a href="dataman.shtml#makeset">Create a set file</a>
<li> <a href="dataman.shtml#tabset">Tabulate SNPs by sets</a>
<li> <a href="dataman.shtml#snp-qual">SNP quality scores</a>
<li> <a href="dataman.shtml#geno-qual">Genotypic quality scores</a>
</ul>
<a href="summary.shtml">7. Summary stats</a>
<ul>
<li> <a href="summary.shtml#missing">Missingness</a>
<li> <a href="summary.shtml#oblig_missing">Obligatory missingness</a>
<li> <a href="summary.shtml#clustermissing">IBM clustering</a>
<li> <a href="summary.shtml#testmiss">Missingness by phenotype</a>
<li> <a href="summary.shtml#mishap">Missingness by genotype</a>
<li> <a href="summary.shtml#hardy">Hardy-Weinberg</a>
<li> <a href="summary.shtml#freq">Allele frequencies</a>
<li> <a href="summary.shtml#prune">LD-based SNP pruning</a>
<li> <a href="summary.shtml#mendel">Mendel errors</a>
<li> <a href="summary.shtml#sexcheck">Sex check</a>
<li> <a href="summary.shtml#pederr">Pedigree errors</a>
</ul>
<a href="thresh.shtml">8. Inclusion thresholds</a>
<ul>
<li> <a href="thresh.shtml#miss2">Missing/person</a>
<li> <a href="thresh.shtml#maf">Allele frequency</a>
<li> <a href="thresh.shtml#miss1">Missing/SNP</a>
<li> <a href="thresh.shtml#hwd">Hardy-Weinberg</a>
<li> <a href="thresh.shtml#mendel">Mendel errors</a>
</ul>
<a href="strat.shtml">9. Population stratification</a>
<ul>
<li> <a href="strat.shtml#cluster">IBS clustering</a>
<li> <a href="strat.shtml#permtest">Permutation test</a>
<li> <a href="strat.shtml#options">Clustering options</a>
<li> <a href="strat.shtml#matrix">IBS matrix</a>
<li> <a href="strat.shtml#mds">Multidimensional scaling</a>
<li> <a href="strat.shtml#outlier">Outlier detection</a>
</ul>
<a href="ibdibs.shtml">10. IBS/IBD estimation</a>
<ul>
<li> <a href="ibdibs.shtml#genome">Pairwise IBD</a>
<li> <a href="ibdibs.shtml#inbreeding">Inbreeding</a>
<li> <a href="ibdibs.shtml#homo">Runs of homozygosity</a>
<li> <a href="ibdibs.shtml#segments">Shared segments</a>
</ul>
<a href="anal.shtml">11. Association</a>
<ul>
<li> <a href="anal.shtml#cc">Case/control</a>
<li> <a href="anal.shtml#fisher">Fisher's exact</a>
<li> <a href="anal.shtml#model">Full model</a>
<li> <a href="anal.shtml#strat">Stratified analysis</a>
<li> <a href="anal.shtml#homog">Tests of heterogeneity</a>
<li> <a href="anal.shtml#hotel">Hotelling's T(2) test</a>
<li> <a href="anal.shtml#qt">Quantitative trait</a>
<li> <a href="anal.shtml#qtmeans">Quantitative trait means</a>
<li> <a href="anal.shtml#qtgxe">Quantitative trait GxE</a>
<li> <a href="anal.shtml#glm">Linear and logistic models</a>
<li> <a href="anal.shtml#set">Set-based tests</a>
<li> <a href="anal.shtml#adjust">Multiple-test correction</a>
</ul>
<a href="fanal.shtml">12. Family-based association</a>
<ul>
<li> <a href="fanal.shtml#tdt">TDT</a>
<li> <a href="fanal.shtml#ptdt">ParenTDT</a>
<li> <a href="fanal.shtml#poo">Parent-of-origin</a>
<li> <a href="fanal.shtml#dfam">DFAM test</a>
<li> <a href="fanal.shtml#qfam">QFAM test</a>
</ul>
<a href="perm.shtml">13. Permutation procedures</a>
<ul>
<li> <a href="perm.shtml#perm">Basic permutation</a>
<li> <a href="perm.shtml#aperm">Adaptive permutation</a>
<li> <a href="perm.shtml#mperm">max(T) permutation</a>
<li> <a href="perm.shtml#rank">Ranked permutation</a>
<li> <a href="perm.shtml#genedropmodel">Gene-dropping</a>
<li> <a href="perm.shtml#cluster">Within-cluster</a>
<li> <a href="perm.shtml#mkphe">Permuted phenotypes files</a>
</ul>
<a href="ld.shtml">14. LD calculations</a>
<ul>
<li> <a href="ld.shtml#ld1">2 SNP pairwise LD</a>
<li> <a href="ld.shtml#ld2">N SNP pairwise LD</a>
<li> <a href="ld.shtml#tags">Tagging options</a>
<li> <a href="ld.shtml#blox">Haplotype blocks</a>
</ul>
<a href="haplo.shtml">15. Multimarker tests</a>
<ul>
<li> <a href="haplo.shtml#hap1">Imputing haplotypes</a>
<li> <a href="haplo.shtml#precomputed">Precomputed lists</a>
<li> <a href="haplo.shtml#hap2">Haplotype frequencies</a>
<li> <a href="haplo.shtml#hap3">Haplotype-based association</a>
<li> <a href="haplo.shtml#hap3c">Haplotype-based GLM tests</a>
<li> <a href="haplo.shtml#hap3b">Haplotype-based TDT</a>
<li> <a href="haplo.shtml#hap4">Haplotype imputation</a>
<li> <a href="haplo.shtml#hap5">Individual phases</a>
</ul>
<a href="whap.shtml">16. Conditional haplotype tests</a>
<ul>
<li> <a href="whap.shtml#whap1">Basic usage</a>
<li> <a href="whap.shtml#whap2">Specifying type of test</a>
<li> <a href="whap.shtml#whap3">General haplogrouping</a>
<li> <a href="whap.shtml#whap4">Covariates and other SNPs</a>
</ul>
<a href="proxy.shtml">17. Proxy association</a>
<ul>
<li> <a href="proxy.shtml#proxy1">Basic usage</a>
<li> <a href="proxy.shtml#proxy2">Refining a signal</a>
<li> <a href="proxy.shtml#proxy2b">Multiple reference SNPs</a>
<li> <a href="proxy.shtml#proxy3">Haplotype-based SNP tests</a>
</ul>
<a href="pimputation.shtml">18. Imputation (beta)</a>
<ul>
<li> <a href="pimputation.shtml#impute1">Making reference set</a>
<li> <a href="pimputation.shtml#impute2">Basic association test</a>
<li> <a href="pimputation.shtml#impute3">Modifying parameters</a>
<li> <a href="pimputation.shtml#impute4">Imputing discrete calls</a>
<li> <a href="pimputation.shtml#impute5">Verbose output options</a>
</ul>
<a href="dosage.shtml">19. Dosage data</a>
<ul>
<li> <a href="dosage.shtml#format">Input file formats</a>
<li> <a href="dosage.shtml#assoc">Association analysis</a>
<li> <a href="dosage.shtml#output">Outputting dosage data</a>
</ul>
<a href="metaanal.shtml">20. Meta-analysis</a>
<ul>
<li> <a href="metaanal.shtml#basic">Basic usage</a>
<li> <a href="metaanal.shtml#opt">Misc. options</a>
</ul>
<a href="annot.shtml">21. Annotation</a>
<ul>
<li> <a href="annot.shtml#basic">Basic usage</a>
<li> <a href="annot.shtml#opt">Misc. options</a>
</ul>
<a href="clump.shtml">22. LD-based results clumping</a>
<ul>
<li> <a href="clump.shtml#clump1">Basic usage</a>
<li> <a href="clump.shtml#clump2">Verbose reporting</a>
<li> <a href="clump.shtml#clump3">Combining multiple studies</a>
<li> <a href="clump.shtml#clump4">Best single proxy</a>
</ul>
<a href="grep.shtml">23. Gene-based report</a>
<ul>
<li> <a href="grep.shtml#grep1">Basic usage</a>
<li> <a href="grep.shtml#grep2">Other options</a>
</ul>
<a href="epi.shtml">24. Epistasis</a>
<ul>
<li> <a href="epi.shtml#snp">SNP x SNP</a>
<li> <a href="epi.shtml#case">Case-only</a>
<li> <a href="epi.shtml#gene">Gene-based</a>
</ul>
<a href="cnv.shtml">25. Rare CNVs</a>
<ul>
<li> <a href="cnv.shtml#format">File format</a>
<li> <a href="cnv.shtml#maps">MAP file construction</a>
<li> <a href="cnv.shtml#loading">Loading CNVs</a>
<li> <a href="cnv.shtml#olap_check">Check for overlap</a>
<li> <a href="cnv.shtml#type_filter">Filter on type </a>
<li> <a href="cnv.shtml#gene_filter">Filter on genes </a>
<li> <a href="cnv.shtml#freq_filter">Filter on frequency </a>
<li> <a href="cnv.shtml#burden">Burden analysis</a>
<li> <a href="cnv.shtml#burden2">Geneset enrichment</a>
<li> <a href="cnv.shtml#assoc">Mapping loci</a>
<li> <a href="cnv.shtml#reg-assoc">Regional tests</a>
<li> <a href="cnv.shtml#qt-assoc">Quantitative traits</a>
<li> <a href="cnv.shtml#write_cnvlist">Write CNV lists</a>
<li> <a href="cnv.shtml#report">Write gene lists</a>
<li> <a href="cnv.shtml#groups">Grouping CNVs </a>
</ul>
<a href="gvar.shtml">26. Common CNPs</a>
<ul>
<li> <a href="gvar.shtml#cnv2"> CNPs/generic variants</a>
<li> <a href="gvar.shtml#cnv2b"> CNP/SNP association</a>
</ul>
<a href="rfunc.shtml">27. R-plugins</a>
<ul>
<li> <a href="rfunc.shtml#rfunc1">Basic usage</a>
<li> <a href="rfunc.shtml#rfunc2">Defining the R function</a>
<li> <a href="rfunc.shtml#rfunc2b">Example of debugging</a>
<li> <a href="rfunc.shtml#rfunc3">Installing Rserve</a>
</ul>
<a href="psnp.shtml">28. Annotation web-lookup</a>
<ul>
<li> <a href="psnp.shtml#psnp1">Basic SNP annotation</a>
<li> <a href="psnp.shtml#psnp2">Gene-based SNP lookup</a>
<li> <a href="psnp.shtml#psnp3">Annotation sources</a>
</ul>
<a href="simulate.shtml">29. Simulation tools</a>
<ul>
<li> <a href="simulate.shtml#sim1">Basic usage</a>
<li> <a href="simulate.shtml#sim2">Resampling a population</a>
<li> <a href="simulate.shtml#sim3">Quantitative traits</a>
</ul>
<a href="profile.shtml">30. Profile scoring</a>
<ul>
<li> <a href="profile.shtml#prof1">Basic usage</a>
<li> <a href="profile.shtml#prof2">SNP subsets</a>
<li> <a href="profile.shtml#dose">Dosage data</a>
<li> <a href="profile.shtml#prof3">Misc options</a>
</ul>
<a href="ids.shtml">31. ID helper</a>
<ul>
<li> <a href="ids.shtml#ex">Overview/example</a>
<li> <a href="ids.shtml#intro">Basic usage</a>
<li> <a href="ids.shtml#check">Consistency checks</a>
<li> <a href="ids.shtml#alias">Aliases</a>
<li> <a href="ids.shtml#joint">Joint IDs</a>
<li> <a href="ids.shtml#lookup">Lookups</a>
<li> <a href="ids.shtml#replace">Replace values</a>
<li> <a href="ids.shtml#match">Match files</a>
<li> <a href="ids.shtml#qmatch">Quick match files</a>
<li> <a href="ids.shtml#misc">Misc.</a>
</ul>
<a href="res.shtml">32. Resources</a>
<ul>
<li> <a href="res.shtml#hapmap">HapMap (PLINK format)</a>
<li> <a href="res.shtml#teach">Teaching materials</a>
<li> <a href="res.shtml#mmtests">Multimarker tests</a>
<li> <a href="res.shtml#sets">Gene-set lists</a>
<li> <a href="res.shtml#glist">Gene range lists</a>
<li> <a href="res.shtml#attrib">SNP attributes</a>
</ul>
<a href="flow.shtml">33. Flow-chart</a>
<ul>
<li> <a href="flow.shtml">Order of commands</a>
</ul>
<a href="misc.shtml">34. Miscellaneous</a>
<ul>
<li> <a href="misc.shtml#opt">Command options/modifiers</a>
<li> <a href="misc.shtml#output">Association output modifiers</a>
<li> <a href="misc.shtml#species">Different species</a>
<li> <a href="misc.shtml#bugs">Known issues</a>
</ul>
<a href="faq.shtml">35. FAQ & Hints</a>
</p>
<a href="gplink.shtml">36. gPLINK</a>
<ul>
<li> <a href="gplink.shtml">gPLINK mainpage</a>
<li> <a href="gplink_tutorial/index.html">Tour of gPLINK</a>
<li> <a href="gplink.shtml#overview">Overview: using gPLINK</a>
<li> <a href="gplink.shtml#locrem">Local versus remote modes</a>
<li> <a href="gplink.shtml#start">Starting a new project</a>
<li> <a href="gplink.shtml#config">Configuring gPLINK</a>
<li> <a href="gplink.shtml#plink">Initiating PLINK jobs</a>
<li> <a href="gplink.shtml#view">Viewing PLINK output</a>
<li> <a href="gplink.shtml#hv">Integration with Haploview</a>
<li> <a href="gplink.shtml#down">Downloading gPLINK</a></p>
</ul>
</font>
</td><td width=5%>
<td valign="top">
</p>
<h1>Resources available for download</h1>
This page contains links to several freely-available resources, mostly
generated by other individuals. All these resources are provided "as
is", without any guarantees regarding their correctness or utility.
<a name="hapmap">
<h2>The Phase 2 HapMap as a PLINK fileset</h2></a>
</p>
The <a href="http://www.hapmap.org">HapMap</a> genotype data (the latest is release
23) are available here as PLINK binary filesets. The SNPs are
currently coded according NCBI build 36 coordinates on the forward
strand. Several versions are available here: the entire dataset (a
single, very large fileset: you will need a computer with at least 2Gb
of RAM to load this file).
</p>
The <em>filtered</em> SNP set refers to a list of SNPs that have MAF
greater than 0.01 and genotyping rate greater than 0.95 in the 60 CEU
founders. This fileset is probably a good starting place for
imputation in samples of European descent. Filtered versions of the
other HapMap panels will be made available shortly.
<table border=1>
<tr>
<td><em><b>Description</b></em></td>
<td><em><b>File size</b></em></td>
<td><em><b>File name</b></em></td>
</tr>
<tr>
<td>Entire HapMap (release 23, 270 individuals, 3.96 million SNPs)</td>
<td> 120M </td>
<td> <a href="dist/hapmap_r23a.zip">hapmap_r23a.zip</a></td>
</tr>
<tr>
<td>CEU (release 23, 90 individuals, 3.96 million SNPs)</td>
<td> 59M </td>
<td> <a href="dist/hapmap_CEU_r23a.zip">hapmap_CEU_r23a.zip</a></td>
</tr>
<tr>
<td>YRI (release 23, 90 individuals, 3.88 million SNPs)</td>
<td> 65M </td>
<td> <a href="dist/hapmap_YRI_r23a.zip">hapmap_YRI_r23a.zip</a></td>
</tr>
<tr>
<td>JPT+CHB (release 23, 90 individuals, 3.99 million SNPs)</td>
<td> 58M </td>
<td> <a href="dist/hapmap_JPT_CHB_r23a.zip">hapmap_JPT_CHB_r23a.zip</a></td>
</tr>
<tr>
<td>CEU founders (release 23, 60 individuals, filtered 2.3 million SNPs)</td>
<td> 31M </td>
<td> <a href="dist/hapmap_CEU_r23a_filtered.zip">hapmap_CEU_r23a_filtered.zip</a></td>
</tr>
<tr>
<td>YRI founders (release 23, 60 individuals, filtered 2.6 million SNPs)</td>
<td> 38M </td>
<td> <a href="dist/hapmap_YRI_r23a_filtered.zip">hapmap_YRI_r23a_filtered.zip</a></td>
</tr>
<tr>
<td>JPT+CHB founders (release 23, 90 individuals, filtered 2.2 million SNPs)</td>
<td> 33M </td>
<td> <a href="dist/hapmap_JPT_CHB_r23a_filtered.zip">hapmap_JPT_CHB_r23a_filtered.zip</a></td>
</tr>
</table>
<br>
<br>
<table border=1>
<tr>
<td><em><b>Description</b></em></td>
<td><em><b>File size</b></em></td>
<td><em><b>File name</b></em></td>
</tr>
<tr>
<td>Entire HapMap (release 22, 270 individuals, 3.96 million SNPs)</td>
<td> 110M </td>
<td> <a href="dist/hapmap_r22.zip">hapmap_r22.zip</a> </td>
</tr>
<tr>
<td>CEU founders (release 22, 60 individuals, 3.96 million SNPs)</td>
<td> 49M </td>
<td> <a href="dist/hapmap-ceu-all.zip">hapmap-ceu-all.zip</a> </td>
</tr>
<tr>
<td>CEU founders (release 22, 60 individuals, filtered 2.2 million SNPs)</td>
<td> 29M </td>
<td> <a href="dist/hapmap-ceu.zip">hapmap-ceu.zip</a> </td>
</tr>
<tr>
<td>CEU founders (release 22, as above, files split by chromosome, 1-22 and X)</td>
<td> 29M </td>
<td> <a href="dist/hapmap-ceu-by-chr.zip">hapmap-ceu-by-chr.zip</a> </td>
</tr>
</table>
<br>
<br>
<table border=1>
<tr>
<td><em><b>Description</b></em></td>
<td><em><b>File name</b></em></td>
</tr>
<tr>
<td>Hapmap individuals with population information ( FID, IID, POP )</td>
<td> <a href="dist/hapmap.pop">hapmap.pop</a> </td>
</tr>
</table>
<a name="teach">
<h2>Teaching materials and example dataset</h2></a>
</p>
A tutorial can be downloaded from here; the material is similar to the
online tutorial but slightly more involved. As it currently stands, it
is designed to first use <em>gPLINK</em> to perform a set of basic
tests and QC procedures and then move to standard <em>PLINK</em> for
more in-depth analysis.
</p>
It is designed to work on a standard modern laptop computer or
equivalent desktop. It was written for vesion 1.02 of PLINK, but
should remain compatible with future releases.
</p>
<table border=1>
<tr>
<td><em><b>Description</b></em></td>
<td><em><b>File size</b></em></td>
<td><em><b>File name</b></em></td>
</tr>
<tr>
<td>ZIP archive containing data</td>
<td> 15M </td>
<td> <a href="dist/example.zip">example.zip</a> </td>
</tr>
<tr>
<td>ZIP archive containing teaching materials</td>
<td> 1.3M </td>
<td> <a href="dist/teaching.zip">teaching.zip</a> </td>
</tr>
</table>
You are feel free to use, modify or distribute these files in any way
you wish, although giving me appropriate credit for the materials
would be appreciated.
</p>
The <tt>example.zip</tt> archive contains
<pre>
wgas1.ped Whole-genome SNP data example PED file
wgas1.map Corresponding MAP file
extra.ped Follow-up genotyping for a particular region
extra.map Corresponding MAP file
pop.cov Population membership variable
command-list.txt List of all commands for 2nd part of practical
</pre>
The <tt>teaching.zip</tt> archive contains a PowerPoint and a Word file:
<pre>
practical-1-slides.ppt
practical-2-notes.doc
</pre>
These two files cover the first and second half of the tutorial
respectively. The second document assumes the first half has already
been completed (but also contains some introductory remarks concerning
the data). I will probably update the Word document to also include
the early commands covered in the PowerPoint/gPLINK part (i.e. so that
the entire practical can be performed from the command line rather
than using gPLINK). The list of commands (<tt>command-list.txt</tt>) is
included so that people can cut-and-paste commands in, rather than type. If
using DOS, it is a good idea to first increase the window width (right click on
header on DOS window, Properties, Layout and increase buffer and window width to
around 120 characters).
</p>
Everything should be fairly self-explantory after looking through the PowerPoint file
and Word document.
<a name="mmtests">
<h2>Multimarker test lists</h2></a>
</p>
These files, generated by Itsik Pe'er and others, facilitate the
'multi-marker predictor' approach to association testing, as described
in the manusctipt:
<pre>
Pe'er I, de Bakker PI, Maller J, Yelensky R, Altshuler D
& Daly MJ (2006) Evaluating and improving power in whole-genome
association studies using fixed marker sets. Nat Genet, 38(6): 605-6.
</pre>
They are PLINK-formatted lists of multimarker tests selected for
Affymetrix 500K and Illumina whole genome products, based on
consideration of the CEU Phase 2 HapMap (at r-squared=0.8
threshold). One should download the appropriate file and run with
the <tt>--hap</tt> option (after ensuring that any strand issues have
been resolved).
<ul>
<li>
<a href="../dist/mmtests/Affymetrix.GeneChip.500k.both.CEU.0.8.tests.zip">
Affymetrix.GeneChip.500k.both.CEU.0.8.tests.zip
</a>
<li>
<a href="../dist/mmtests/Illumina.HumanHap.300k.CEU.0.8.tests.zip">
Illumina.HumanHap.300k.CEU.0.8.tests.zip
</a>
<li>
<a href="../dist/mmtests/Illumina.HumanHap.550k.CEU.0.8.tests.zip">
Illumina.HumanHap.550k.CEU.0.8.tests.zip
</a>
<li>
<a href="../dist/mmtests/Illumina.HumanHap.650k.CEU.0.8.tests.zip">
Illumina.HumanHap.650k.CEU.0.8.tests.zip
</a>
</ul>
<strong>Note</strong> These haplotypes are specified in terms
of the +ve (positive) strand relative to the HapMap. You might need to
reformat your data prior to using these files (using the
<tt>--flip</tt> command, for instance) before you can use them.
</p>
<strong>Note</strong> These tables list all tags for every common HapMap
SNP, at the given r-squared threshold. The same haplotype may therefore
appear multiple times (i.e. if it tags more than 1 SNP).
</p>
<strong>Note</strong> These tables obviously assume that all tags on present in
the final, post-quality-control dataset: i.e. if certain SNPs have been removed,
it will be better to reselect the predictors -- that is, these lists should really
only be used as a first pass, for convenience.
</p>
In general, however, quite possibily an easier and better strategy is
instead to analyse the data within
an <a href="pimputation.shtml">imputation context</a>, e.g. utilising
the proxy association procedures rather than using these fixed lists.
<a name="sets">
<h2>Gene sets</h2></a>
</p>
<strong>NOTE</strong> The gene range lists below have replaced this old gene SET file:
you are advised to use the lists <a href="#glist">below</a> rather than this file.
</p>
Here is a <tt>PLINK</tt>-format <a href="data.shtml#sets">SET
file</a>, containing a genome-wide set of genes (N=18272). The
co-ordinates are based on NCBI B36 assembly, dbSNP 126; a gene is
arbitrarily defined as including 50kb upstream and downstream.
</p>
<tt> Download (ZIP archive): </tt>
<a href="dist/gene-list.zip">gene-list.zip</a>
</p>
<a name="glist">
<h2>Gene range lists</h2></a>
</p>
These are gene lists: files containing lists of genes, based on either
hg17 or hg18 co-ordinates. The format is one gene per row,
<pre>
Chromosome
Start position (bp)
Stop position (bp)
Gene name
</pre>
These lists can be used with PLINK commands such as
<tt>--make-set</tt>, <tt>--range</tt>, <tt>--gene-list</tt>,
<tt>--cnv-intersect</tt>, <tt>--clump-range</tt>, etc.
<p>
These gene lists were downloaded from UCSC table browser for all
RefSeq genes on July 24th 2008. Overlapping isoforms of the same gene
were combined to form a single full length version of the gene.
Isoforms that didn't overlap were left as duplicates of that gene.
</p>
Rather than using the gene sets
(described <a href="res.shtml#sets">above</a>), we suggest using these
gene lists to make gene sets on the fly
(using <tt>--make-set-border</tt> if so desired, to add a fixed kb
border on the fly).
</p>
<tt> Gene list (hg18): </tt> <a href="dist/glist-hg18">glist-hg18</a> <br>
<tt> Gene list (hg17): </tt> <a href="dist/glist-hg17">glist-hg17</a>
</p>
<a name="attrib">
<h2>Functional SNP attributes</h2></a>
</p>
This file contains a list of codes to indicate the functional status of SNPs. It is designed to be
used in conjunction with the <a href="annot.shtml"><tt>--annotate</tt></a> command.
</p>
This file was created as follows: we downloaded all data from dbSNP,
build 129, and extracted lists of SNPs that are nonsense, frameshift,
missense or splice-site variants. We intersected this list with the
SNPs available in the Phase 2 CEU HapMap dataset, and selected lists
of SNPs that strongly tagged this functional SNPs (r-sq above 0.5; MAF
above 0.01). For each HapMap SNP that either is or tags a functional
SNP, we created an entry in the file below. Here upper-case represents
that that SNP is a coding SNP in HapMap; lower-case represents that
the SNP is in strong LD with a coding variant, in HapMap.
<pre>
=NONSENSE =nonsense
=MISSENSE =missense
=FRAMESHIFT =frameshift
=SPLICE =splice
</pre>
In future, we will post revised attribute files, to include more
annotations, and information (e.g. such as a version with the rs ID of
the functional SNP(s) that is tagged).
</p>
<tt> SNP attributes: </tt> <a href="dist/snp129.attrib.gz">snp129.attrib.gz</a> <br>
</p>
To use the file with the <tt>--annotate</tt> command, for example:
<pre>
plink --annotate myresults.txt attrib=snp129.attrib.gz
</pre>
(You can use <tt>gunzip</tt>, or WinZip, to decompress this file.)
</td>
<td width=5%> </td>
</tr>
</table>
<hr>
<em>
This document last modified Wednesday, 25-Jan-2017 11:39:28 EST
</em>
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