From 076ec2ac8a7b1488476454c36b6a23255bed1529 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 11 Feb 2020 12:11:37 +0000
Subject: [PATCH] JAL-3376 documentation for standard attributes for variants
 from VCF

---
 help/help/help.jhm                     |    1 +
 help/help/helpTOC.xml                  |    2 +-
 help/help/html/features/importvcf.html |   23 +++++++++++++++++++++++
 3 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 47f7d53..6b0a1c0 100755
--- 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
index 7e358d6..5374e1a 100755
--- 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
index e013472..511ff2e 100755
--- a/help/help/html/features/importvcf.html
+++ b/help/help/html/features/importvcf.html
@@ -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>
-- 
1.7.10.2