X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fimportvcf.html;h=7b699eb3462c3d104eaf623410f76caa1f0805d7;hb=cfcd397b19f70fb39d6d21437db8eb6ffcac3914;hp=e013472883ba26f3a37c4972b0a8c044deab15d1;hpb=dd193c9ceff22f721c53814fd9c37f269a9edfde;p=jalview.git

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 +49,47 @@
     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>