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>
##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
</ol>
<strong>Work in Progress!</strong>
<p>VCF support in Jalview is under active development. Please get
- in touch via our mailing list if you have any questions, problems or
+ in touch via our discussion forum if you have any questions, problems or
otherwise find it useful !</p>
</body>
</html>