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<!doctype html>
<html lang="en">
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<div class="container theme-showcase" role="main">
<div class="page-header">
<h1>GLIMPSE command options</h1>
</div>
<h4>
<p><b>Tool name:</b></p>
<p><a href="#chunk"><span class="label label-success" style="display:inline-block; width:130px; height:22px;">GLIMPSE chunk</span></a> defines chunks where to run imputation</p>
<p><a href="#phase"><span class="label label-primary" style="display:inline-block; width:130px;">GLIMPSE phase</span></a> main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods</p>
<p><a href="#ligate"><span class="label label-info" style="display:inline-block; width:130px;">GLIMPSE ligate</span></a> concatenate imputation chunks in a single VCF/BCF file ligating phased information</p>
<p><a href="#sample"><span class="label label-warning" style="display:inline-block; width:130px;">GLIMPSE sample</span></a> generate haplotype calls by sampling haplotype estimates</p>
<hr>
<p><b>Detailed description</b></p>
</h4>
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<a id="chunk"></a>
<div class="panel panel-success">
<div class="panel-heading">
<h3 class="panel-title">GLIMPSE chunk</h3>
</div>
<div class="panel-body">
<h4>Usage</h4>
<code>GLIMPSE_chunk --input input.GLs.vcf.gz --reference reference.bcf --region chr20 --window-size 2000000 --window-count 2000 --buffer-size 500000 --buffer-count 500 --output chunks.txt --log chunks.log </code>
<table class="table table-striped">
<col width="15%">
<col width="10%">
<col width="10%">
<col width="65%">
<h4>Command options</h4>
<thead>
<tr>
<th>Long form</th>
<th>Short</th>
<th>Argument</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>--help</code></td>
<td>NA</td>
<td>NA</td>
<td>Produces an help message with a short description of the command options</td>
</tr>
<tr>
<td><code>--seed</code></td>
<td>NA</td>
<td>INT</td>
<td>Seed for random number generator.</td>
</tr>
<tr>
<td><code>--input</code></td>
<td><code>--I</code></td>
<td>STRING</td>
<td>Input VCF/BCF file containing genotype likelihoods</td>
</tr>
<tr>
<td><code>--reference</code></td>
<td><code>--R</code></td>
<td>STRING</td>
<td>Reference panel file possibly with or without GT field (for efficiency reasons a file containing only the positions of the reference panel is recommended).</td>
</tr>
<tr>
<td><code>--region</code></td>
<td>NA</td>
<td>STRING</td>
<td>Target region (e.g. chr20:1000000-2000000 or chr20).</td>
</tr>
<tr>
<td><code>--window-size</code></td>
<td>NA</td>
<td>INT</td>
<td>Minimal size of the imputation region in basepairs.</td>
</tr>
<tr>
<td><code>--window-count</code></td>
<td>NA</td>
<td>INT</td>
<td>Minimal number of variants present in the imputation region.</td>
</tr>
<tr>
<td><code>--buffer-size</code></td>
<td>NA</td>
<td>INT</td>
<td>Minimal size of the buffer region in basepairs.</td>
</tr>
<tr>
<td><code>--buffer-count</code></td>
<td>NA</td>
<td>INT</td>
<td>Minimal number of variants present in the buffer region.</td>
</tr>
<tr>
<td><code>--output</code></td>
<td><code>-O</code></td>
<td>STRING</td>
<td>Output file containing buffer and imputation regions.</td>
</tr>
<tr>
<td><code>--log</code></td>
<td>NA</td>
<td>STRING</td>
<td>Log file.</td>
</tr>
</tbody>
</table>
</div>
</div>
<a id="phase"></a>
<div class="panel panel-primary">
<div class="panel-heading">
<h3 class="panel-title">GLIMPSE phase</h3>
</div>
<div class="panel-body">
<h4>Usage</h4>
<code>GLIMPSE_phase --input input.GLs.vcf.gz --reference reference.bcf --region chr20 --thread 8 --input-region chr20:1500000-4500000 --map chr20.b38.gmap.gz --output-region chr20:2000000-4000000 --output imputed.chunk1.bcf --log imputed.chunk1.log </code>
<table class="table table-striped">
<col width="15%">
<col width="10%">
<col width="10%">
<col width="65%">
<h4>Command options</h4>
<thead>
<tr>
<th>Long form</th>
<th>Short</th>
<th>Argument</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>--help</code></td>
<td>NA</td>
<td>NA</td>
<td>Produces an help message with a short description of the command options</td>
</tr>
<tr>
<td><code>--seed</code></td>
<td>NA</td>
<td>INT</td>
<td>Seed for random number generator.</td>
</tr>
<tr>
<td><code>--thread</code></td>
<td>NA</td>
<td>INT</td>
<td>Number of threads to use (default 1).</td>
</tr>
<tr>
<td><code>--input</code></td>
<td><code>--I</code></td>
<td>STRING</td>
<td>Input VCF/BCF file containing genotype likelihoods</td>
</tr>
<tr>
<td><code>--reference</code></td>
<td><code>--R</code></td>
<td>STRING</td>
<td>Reference panel of haplotypes in VCF/BCF format.</td>
</tr>
<tr>
<td><code>--input-region</code></td>
<td>NA</td>
<td>STRING</td>
<td>Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).</td>
</tr>
<tr>
<td><code>--map</code></td>
<td><code>--M</code></td>
<td>STRING</td>
<td>File containing the genetic map.</td>
</tr>
<tr>
<td><code>--burnin</code></td>
<td>NA</td>
<td>INT</td>
<td>Number of burn-in iterations of the Gibbs sampler.</td>
</tr>
<tr>
<td><code>--main</code></td>
<td>NA</td>
<td>INT</td>
<td>Number of main iterations of the Gibbs sampler. Each main iterations cotributes to output genotypes. Haplotypes sampled for the last (max 16) iterations are stored in the HS field.</td>
</tr>
<tr>
<td><code>--pbwt-depth</code></td>
<td>NA</td>
<td>INT</td>
<td>Depth of PBWT indexes to condition on.</td>
</tr>
<tr>
<td><code>--pbwt-modulo</code></td>
<td>NA</td>
<td>INT</td>
<td>Frequency of PBWT selection.</td>
</tr>
<tr>
<td><code>--init-states</code></td>
<td>NA</td>
<td>INT</td>
<td>Number of states used for initialization and maximal number of states in the subsequent iterations.</td>
</tr>
<tr>
<td><code>--init-pool</code></td>
<td>NA</td>
<td>INT</td>
<td>List of samples (sample IDs) from which haplotypes are initialised.</td>
</tr>
<tr>
<td><code>--ne</code></td>
<td>NA</td>
<td>FLOAT</td>
<td>Effective diploid population size.</td>
</tr>
<tr>
<td><code>--output</code></td>
<td><code>-O</code></td>
<td>STRING</td>
<td>Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.</td>
</tr>
<tr>
<td><code>--output-region</code></td>
<td>NA</td>
<td>STRING</td>
<td>Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).</td>
</tr>
<tr>
<td><code>--log</code></td>
<td>NA</td>
<td>STRING</td>
<td>Log file.</td>
</tr>
</tbody>
</table>
</div>
</div>
<a id="ligate"></a>
<div class="panel panel-info">
<div class="panel-heading">
<h3 class="panel-title">GLIMPSE ligate</h3>
</div>
<div class="panel-body">
<h4>Usage</h4>
<code>GLIMPSE_ligate --input list.imputed.txt --output imputed.chr20.bcf --log imputed.chr20.log</code>
<table class="table table-striped">
<col width="15%">
<col width="10%">
<col width="10%">
<col width="65%">
<h4>Command options</h4>
<thead>
<tr>
<th>Long form</th>
<th>Short</th>
<th>Argument</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>--help</code></td>
<td>NA</td>
<td>NA</td>
<td>Produces an help message with a short description of the command options</td>
</tr>
<tr>
<td><code>--seed</code></td>
<td>NA</td>
<td>INT</td>
<td>Seed for random number generator.</td>
</tr>
<tr>
<td><code>--input</code></td>
<td><code>--I</code></td>
<td>STRING</td>
<td>Text file containing the full list of files to ligate (one file per line)</td>
</tr>
<tr>
<td><code>--output</code></td>
<td><code>-O</code></td>
<td>STRING</td>
<td>Output VCF/BCF file for the merged regions. Phased information (HS field) is updated accordingly for the full region.</td>
</tr>
<tr>
<td><code>--log</code></td>
<td>NA</td>
<td>STRING</td>
<td>Log file.</td>
</tr>
</tbody>
</table>
</div>
</div>
<a id="sample"></a>
<div class="panel panel-warning">
<div class="panel-heading">
<h3 class="panel-title">GLIMPSE sample</h3>
</div>
<div class="panel-body">
<h4>Usage</h4>
<code>GLIMPSE_sample --input imputed.chr20.bcf --sample --output phased.chr20.bcf --log phased.chr20.log </code>
<table class="table table-striped">
<col width="15%">
<col width="10%">
<col width="10%">
<col width="65%">
<h4>Command options</h4>
<thead>
<tr>
<th>Long form</th>
<th>Short</th>
<th>Argument</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>--help</code></td>
<td>NA</td>
<td>NA</td>
<td>Produces an help message with a short description of the command options</td>
</tr>
<tr>
<td><code>--seed</code></td>
<td>NA</td>
<td>INT</td>
<td>Seed for random number generator.</td>
</tr>
<tr>
<td><code>--input</code></td>
<td><code>--I</code></td>
<td>STRING</td>
<td>VCF/BCF file generated using <i>GLIMPSE ligate</i></td>
</tr>
<tr>
<td><code>--sample</code></td>
<td>NA</td>
<td>STRING</td>
<td>Sample a likely haplotype pair for each sample (to be used in combination with <code>--seed</code> option) </td>
</tr>
<tr>
<td><code>--solve</code></td>
<td>NA</td>
<td>STRING</td>
<td>Get the most likely haplotype pair for each sample (the random number generator is not used)</td>
</tr>
<tr>
<td><code>--output</code></td>
<td><code>-O</code></td>
<td>STRING</td>
<td>Output VCF/BCF file containing phased genotypes.</td>
</tr>
<tr>
<td><code>--log</code></td>
<td>NA</td>
<td>STRING</td>
<td>Log file.</td>
</tr>
</tbody>
</table>
</div>
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