X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fimportvcf.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fimportvcf.html;h=511ff2e5e2e0683ced84c75cce2b42f08e4cd1ca;hb=076ec2ac8a7b1488476454c36b6a23255bed1529;hp=e013472883ba26f3a37c4972b0a8c044deab15d1;hpb=75c5f789efcd5d6a1f61f5795f856f4012c21cca;p=jalview.git

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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>