Merge pull request PGScatalog#346 from fyvon/documentation/scoringfil…

…e_schema_apr2024

Updating scoring file schema with effect/other allele description note (apr2024)

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@@ -93,10 +93,10 @@ <h5 id="scoring_columns" class="mt-5"><i class="fas fa-th pgs_color_1 mr-2"></i>
       <tbody>
         <tr class="table-tr-hl"><td colspan="4"><i class="fas fa-chevron-right pgs_color"></i> Variant Description:</td></tr>
         <tr><td>rsID</td><td>dbSNP Accession ID (rsID)</td><td><span style="cursor:pointer" data-toggle="tooltip" data-placement="right" data-html="true" title="Unless both the <b>chr_name</b> and <b>chr_position</b> columns are absent"><span class="badge pgs_bg_color_amber">Optional</span> <span class="fas fa-info-circle pgs_color_1"></span></span></td><td>The SNP’s rs ID.<br/>This column also contains HLA alleles in the standard notation (e.g. HLA-DQA1*0102) that aren’t always provided with chromosomal positions.</td></tr>
-        <tr><td>chr_name</td><td>Location - Chromosome </td><td><span style="cursor:pointer" data-toggle="tooltip" data-placement="right" data-html="true" title="May be optional if an <b>rsID</b> for the variant is provided"><span class="badge pgs_bg_color_red">Required</span> <span class="fas fa-info-circle pgs_color_1"></span></span></td><td>Chromosome name/number associated with the variant</td></tr>
-        <tr><td>chr_position</td><td>Location within the Chromosome</td><td><span style="cursor:pointer" data-toggle="tooltip" data-placement="right" data-html="true" title="May be optional if an <b>rsID</b> for the variant is provided"><span class="badge pgs_bg_color_red">Required</span> <span class="fas fa-info-circle pgs_color_1"></span></span></td><td>Chromosomal position associated with the variant</td></tr>
-        <tr><td>effect_allele</td><td>Effect Allele</td><td><span class="badge pgs_bg_color_red">Required</span></td><td>The allele that's dosage is counted (e.g. {0, 1, 2}) and multiplied by the variant's weight (<b>effect_weight</b>) when calculating score. The effect allele is also known as the 'risk allele'.</td></tr>
-        <tr><td>other_allele</td><td>Other allele(s)</td><td><span style="cursor:pointer" data-toggle="tooltip" data-placement="right" data-html="true" title="Optional, however this column is strongly recommended"><span class="badge pgs_bg_color_amber">Recommended</span> <span class="fas fa-info-circle pgs_color_1"></span></span></td><td>The other allele(s) at the loci</td></tr>
+        <tr><td>chr_name</td><td>Location - Chromosome </td><td><span style="cursor:pointer" data-toggle="tooltip" data-placement="right" data-html="true" title="May be optional if an <b>rsID</b> for the variant is provided"><span class="badge pgs_bg_color_red">Required</span> <span class="fas fa-info-circle pgs_color_1"></span></span></td><td>Chromosome name/number associated with the variant.</td></tr>
+        <tr><td>chr_position</td><td>Location within the Chromosome</td><td><span style="cursor:pointer" data-toggle="tooltip" data-placement="right" data-html="true" title="May be optional if an <b>rsID</b> for the variant is provided"><span class="badge pgs_bg_color_red">Required</span> <span class="fas fa-info-circle pgs_color_1"></span></span></td><td>Chromosomal position associated with the variant.</td></tr>
+        <tr><td>effect_allele</td><td>Effect Allele</td><td><span class="badge pgs_bg_color_red">Required</span></td><td>The allele that's dosage is counted (e.g. {0, 1, 2}) and multiplied by the variant's weight (<b>effect_weight</b>) when calculating score. The effect allele is also known as the 'risk allele'. Note: this does not necessarily need to correspond to the minor allele/alternative allele.</td></tr>
+        <tr><td>other_allele</td><td>Other allele(s)</td><td><span style="cursor:pointer" data-toggle="tooltip" data-placement="right" data-html="true" title="Optional, however this column is strongly recommended"><span class="badge pgs_bg_color_amber">Recommended</span> <span class="fas fa-info-circle pgs_color_1"></span></span></td><td>The other allele(s) at the loci. Note: this does not necessarily need to correspond to the reference allele.</td></tr>
         <tr><td>locus_name</td><td>Locus Name</td><td><span class="badge pgs_bg_color_green">Optional</span></td><td>This is kept in for loci where the variant may be referenced by the gene (APOE e4). It is also common (usually in smaller PGS) to see the variants named according to the genes they impact.</td></tr>
         <tr><td>is_haplotype<br>is_diplotype</td><td>FLAG: Haplotype or Diplotype</td><td><span class="badge pgs_bg_color_green">Optional</span></td><td>This is a TRUE/FALSE variable that flags whether the effect allele is a haplotype/diplotype rather than a single SNP. Constituent SNPs in the haplotype are semi-colon separated. </td></tr>
         <tr><td>imputation_method</td><td>Imputation Method</td><td><span class="badge pgs_bg_color_green">Optional</span></td><td>This described whether the variant was specifically called with a specific imputation or variant calling method. This is mostly kept to describe HLA-genotyping methods (e.g. flag SNP2HLA, HLA*IMP) that gives alleles that are not referenced by genomic position.</td></tr>