Importing Variants from VCF

From: Jim Procter Date: Tue, 2 Jul 2019 14:34:10 +0000 (+0100) Subject: Merge branch 'documentation/JAL-3111_release_211' into develop X-Git-Tag: Release_2_11_0~2^2~14 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=7db05549804d9e41c20dbb340c4b716b35dc6d21;hp=772a0325f9223183aeb978c81d2d9cdcb12100df Merge branch 'documentation/JAL-3111_release_211' into develop --- diff --git a/help/help/help.jhm b/help/help/help.jhm index 1666cc6..64f3d21 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -165,4 +165,6 @@ + + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 77ddd88..a0995c2 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -24,8 +24,9 @@ - - + + + @@ -49,6 +50,7 @@ + diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html new file mode 100755 index 0000000..bbc9f78 --- /dev/null +++ b/help/help/html/features/importvcf.html @@ -0,0 +1,74 @@ + + + +Importing Variants from VCF + + +

+ Importing Genomic Variants from VCF +

+ +

Jalview can annotate nucleotide sequences associated with + genomic loci with features representing variants imported from VCF + files. This new feature in Jalview 2.11, is currently tuned to work + best with tab indexed VCF files produced by the GATK Variant + Annotation Pipeline (with or without annotation provided by the + Ensembl Variant Effect Predictor), but other sources of VCF files + should also work.

+ If your sequences have genomic loci, then a Taxon + name and chromosome location should be shown in + the Sequence Details report and the Sequence ID tooltip (providing + you have enabled it via the submenu in the View + menu). Jalview matches the assembly information provided in the VCF + file to the taxon name, using an internal lookup table. If a match + is found, Jalview employs the Ensembl API's lift-over services to + locate your sequences' loci in the VCF file assembly's reference + frame. If all goes well, after loading a VCF, Jalview will report + the number of variants added as sequence features via the alignment + window's status bar. These are added by default when loci are + retrieved from Ensembl. +

+ Working with variants from organisms other than + H.sapiens. +

Look in your VCF file to identify keywords in the + ##reference header that define what species and assembly name the + VCF was generated against.
Look at ensembl.org to identify the species' short name, + and the assembly's unique.
Add mappings to the VCF_SPECIES and VCF_ASSEMBLY + properties in your .jalview_properties file. For example:
```
+VCF_SPECIES=1000genomes=homo_sapiens,c_elegans=celegans
+VCF_ASSEMBLY=assembly19=GRCh37,hs37=GRCh37
```
These allow + annotations to be mapped from both Human 1000genomes VCF files and + C.elegans files. +

+ Work in Progress! +

VCF support in Jalview is under active development. Please get + in touch via our mailing list if you have any questions, problems or + otherwise find it useful !

+ + diff --git a/help/help/html/menus/alwfile.html b/help/help/html/menus/alwfile.html index 57ffa08..653eeda 100755 --- a/help/help/html/menus/alwfile.html +++ b/help/help/html/menus/alwfile.html @@ -130,12 +130,9 @@ annotations.

Load VCF File
- Load VCF annotations from a plain text or tab-indexed file. -
This option is offered for nucleotide alignments, and requires at least one - sequence to have known genomic coordinates. -
Genomic coordinates are attached to entries retrieved from Ensembl. -
Support for VCF was added in Jalview 2.11. -

+ Load VCF annotations from a plain text, or indexed file (.csi,.tsi). +
Only available for nucleotide alignments, and requires at least one + sequence to have known genomic coordinates.

Close (Control W)
Close the alignment window. Make sure you have saved your alignment before you close - either as a Jalview project or by using the Save diff --git a/help/help/html/releases.html b/help/help/html/releases.html index d6ebd1b..31b957c 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -101,12 +101,17 @@ li:before { implementation that allows updates) used for Sequence Feature collections

- Sequence features can be filtered and - shaded according to any associated attributes (e.g. variant - attributes from VCF file, or key-value pairs imported from - column 9 of GFF file) -
-
+ Sequence + features can be filtered and shaded according to any + associated attributes (e.g. variant attributes from VCF + file, or key-value pairs imported from column 9 of GFF + file) +
+
+ Feature Attributes and shading schemes + stored and restored from Jalview Projects +
+
Use full Sequence Ontology (via BioJava) to recognise variant features
@@ -250,18 +255,36 @@ li:before { Build system migrated from Ant to Gradle
Enhanced checks for missing and duplicated keys in Message bundles
-
- Eclipse project configuration managed with - gradle-eclipse -
-
- Atlassian Bamboo continuous integration for - unattended Test Suite execution
+
+ Eclipse project configuration managed with + gradle-eclipse +
+
+ Atlassian + Bamboo continuous integration for unattended Test Suite + execution +

Memory test suite to detect leaks in common - operations
-
More unit test coverage, and minor issues resolved.
-
Developer documentation migrated to markdown (with HTML rendering)
+ operations + +
+ More unit test coverage, and minor + issues resolved. +
+
+ Developer documentation migrated to + markdown (with HTML rendering) +
+
+ HelpLinksChecker runs on Windows +
+
+ New URLs for publishing development + versions of Jalview +
+
+
@@ -458,7 +481,14 @@ li:before { Sequence.findIndex returns wrong value when sequence's End is greater than its length
- New Known Defects +
Bugs fixed for Java 11 Support (not + yet on general release) +
+
+ Menus work properly in split-screen +
+
+ New Known Defects

Select columns containing feature by double clicking ignores bounds of an existing selected region
@@ -493,14 +523,19 @@ li:before {
F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
-
Java 11 Specific defects +
+ Closing tree windows with CMD/CTRL-W for + alignments with multiple views can close views unexpectedly +
+
Java 11 Specific defects

- Jalview Properties file is not sorted alphabetically when saved
- -
- -
+ Jalview Properties file is not sorted + alphabetically when saved + + + +