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Update Harmonization documentation to make it a bit more clear #290

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Oct 23, 2023
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Update Harmonization documentation to make it a bit more clear #290

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27 changes: 25 additions & 2 deletions catalog/templates/catalog/downloads/harmonized_files.html
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Expand Up @@ -16,7 +16,7 @@ <h4 class="mr-3" id="dl_ftp_scoring_hm_pos">Harmonized Files</h4>
<p>
PGS Scoring Files in the Catalog are currently provided in a consistent format with standardized column names and data types, along with information about the genome build given by authors.
The variant-level information in PGS is often heterogeneously described and may lack chromosome/position information, contain a mix of positions and/or rsIDs, or be mapped to a genome build different from your sample genotypes.
To make PGS easier to apply we have created a new set of files that contain harmonized variant information (chromosome name and base pair position) and variant identifiers (updated rsID), in commonly used genome builds (GRCh37/hg19 and GRCh38/hg38) to make variant matching and PGS calculation easier.
To make PGS easier to apply we have created a new set of files that contain <b>additional columns</b> with harmonized variant information (chromosome name and base pair position) and variant identifiers (updated rsID), in commonly used genome builds (GRCh37/hg19 and GRCh38/hg38) to make variant matching and PGS calculation easier.
</p>
<span>
The generation of these harmonized files is done by using the <a href="https://github.com/PGScatalog/pgs-harmonizer">pgs-harmonizer</a> tool. It is based on the <a href="https://github.com/EBISPOT/gwas-sumstats-harmoniser">Open Targets and GWAS Catalog Summary Statistics harmonizer pipelines</a>. To harmonize the variant positions the pgs-harmonizer performs the following tasks:
Expand Down Expand Up @@ -113,7 +113,7 @@ <h5 id="hm_pos_header" class="mt-5"><i class="fas fa-hashtag pgs_color_1 mr-2"><

<h5 id="hm_pos_columns" class="mt-5"><i class="fas fa-th pgs_color_1 mr-2"></i>Harmonized Files <span class="pgs_color_1">—</span> Additional Columns</h5>

<p>The following columns are appended to the formatted scoring file in each HmPOS file:</p>
<p>The formatted scoring file (in the original genome build) has the following additional columns describing the variants in the <b>specified genome build</b> for each HmPOS file:</p>

<div class="table-responsive">
<table class="table table-striped table_pgs_auto">
Expand All @@ -131,4 +131,27 @@ <h5 id="hm_pos_columns" class="mt-5"><i class="fas fa-th pgs_color_1 mr-2"></i>H
</tbody>
</table>
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<i class="fas fa-angle-double-right pgs_color_1"></i> <a class="toggle_btn pgs_btn_plus" data-toggle="tooltip" data-placement="right" data-delay="500" id="pgs_hm_content_example" title="Click to show/hide an example of Scoring Files header">Example of PGS Harmonized File (<span class="pgs_color_facet_2">GRCh37</span> file harmonized on <span class="pgs_color_facet_3">GRCh38</span>)</a>
<div class="toggle_list mt-2" id="list_pgs_hm_content_example">
<div class="pgs_formatted_block">
<pre class="example">
<span>###PGS CATALOG SCORING FILE - see https://www.pgscatalog.org/downloads/#dl_ftp_scoring for additional information</span>
<b>#format_version</b>=2.0
<span>##POLYGENIC SCORE (PGS) INFORMATION</span>
<b>#pgs_id</b>=PGS000116
<span>...</span>
<b>#genome_build</b>=<span class="pgs_color_2">GRCh37</span>
<span>...</span>
<span>##HARMONIZATION DETAILS</span>
<b>#HmPOS_build</b>=<span class="pgs_color_facet_3">GRCh38</span>
<span>...</span>
<span class="pgs_color_facet_2">rsID</span> <span class="pgs_color_facet_2">chr_name</span> <span class="pgs_color_facet_2">chr_position</span> <span class="scoring_col pr-0">effect_allele</span> <span class="scoring_col pr-0">other_allele</span> <span class="scoring_col pr-0">effect_weight</span> <span class="scoring_col pr-0">hm_source</span> <span class="pgs_color_facet_3">hm_rsID</span> <span class="pgs_color_facet_3">hm_chr</span> <span class="pgs_color_facet_3">hm_pos</span>
rs1921 1 949608 A G -0.003965 ENSEMBL rs1921 1 1014228
rs2710887 1 986443 T C -0.000846 ENSEMBL rs2710887 1 1051063
rs11260596 1 1002434 T C 0.000789 ENSEMBL rs11260596 1 1067054
rs113355263 1 1069535 A G -0.001627 ENSEMBL rs113355263 1 1134155
rs11260539 1 1109903 T C 0.000170 ENSEMBL rs11260539 1 1174523
...</pre>
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