JAL-3376 documentation for standard attributes for variants from VCF

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 47f7d53..6b0a1c0 100755 (executable)
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -167,4 +167,5 @@
    <mapID target="overviewprefs" url="html/features/preferences.html#overview" />
    
    <mapID target="importvcf" url="html/features/importvcf.html" />
+   <mapID target="importvcf.attribs" url="html/features/importvcf.html#attribs" />
 </map>

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
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--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,7 +24,7 @@
        <tocitem text="Jalview Documentation" target="home" expand="true">
                        <tocitem text="What's new" target="new" expand="true">
                                <tocitem text="Latest Release Notes" target="release"/>
-                               <tocitem text="VCF Import" target="importvcf"/>
+                               <tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
                                <tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
                                
                </tocitem>

diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html
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--- a/help/help/html/features/importvcf.html
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@@ -49,6 +49,29 @@
     retrieved from Ensembl.
   </p>
   <p>
+    <strong><a name="attribs">Standard Variant Attributes</a></strong>
+  </p>
+  <p>Jalview decorates variant features imported from VCF files with
+    attributes that can be used to filter or shade variant annotation
+    including the following:
+  </p>
+  <ul>
+    <li><em>POS</em> - Chromosomal position as recorded in VCF</li>
+    <li><em>ID</em> - in GNOMAD releases specifies rs identifier of
+      a known dbSNP variant.</li>
+    <li>QUAL is the 'phred-scaled quality score' for the ALT
+      assertion (or quality of SNP call if there are no alternate
+      alleles). Higher is more confident.</li>
+    <li><em>FILTER</em> is 'PASS' if all filters have been passed,
+      else a list of failed filters for the variant (e.g. poor quality,
+      or insufficient sample size).</li>
+  </ul>
+  <p><em>Standard attributes were introduced in Jalview 2.11.1.0.</em> VCF field semantics are highly dependent on the source of your VCF
+    file. See <a
+      href="https://www.internationalgenome.org/wiki/Analysis/vcf4.0">https://www.internationalgenome.org/wiki/Analysis/vcf4.0</a>
+    for more information.
+  </p>
+  <p>
     <strong>Working with variants from organisms other than
       H.sapiens.</strong>
   </p>