JAL-3407 add and document ComputePeptideVariants.groovy

[jalview.git] / help / help / html / features / importvcf.html

diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html
index bbc9f78..7b699eb 100755 (executable)
--- a/help/help/html/features/importvcf.html
+++ b/help/help/html/features/importvcf.html
@@ -49,6 +49,47 @@
     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 without CSQ fields</strong>
+  </p>
+  <p>
+    <a name="computepepvariants">Jalview 2.11.1's new virtual
+      features</a> mean that peptide sequences are no longer annotated
+    directly with protein missense variants. This makes it harder to
+    filter variants when they do not already include the CSQ field. You
+    can rescue the pre-2.11.1 functionality by:
+  </p>
+  <ol>
+    <li>Download the script at
+      https://www.jalview.org/examples/groovy/ComputePeptideVariants.groovy</li>
+    <li>Executing the script via the <a href="groovy.html">Groovy
+        Console</a> on a linked CDS/Protein view to create missense and
+      synonymous peptide variant features.
+    </li>
+  </ol>
+  <p>
     <strong>Working with variants from organisms other than
       H.sapiens.</strong>
   </p>
@@ -57,7 +98,7 @@
       ##reference header that define what species and assembly name the
       VCF was generated against.</li>
     <li>Look at ensembl.org to identify the species' short name,
-      and the assembly's unique.</li>
+      and the assembly's unique id.</li>
     <li>Add mappings to the <strong>VCF_SPECIES</strong> and <strong>VCF_ASSEMBLY</strong>
       properties in your .jalview_properties file. For example:<pre>
 VCF_SPECIES=1000genomes=homo_sapiens,c_elegans=celegans