Importing Variants from VCF

From 7bb2a1c049e7b7be9c04012ce90afc173b81eb1a Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 2 Jul 2019 15:28:19 +0100 Subject: [PATCH] JAL-3111 whats new and JAL-2738 JAL-2743 expanded help documentation for VCF --- help/help/help.jhm | 2 + help/help/helpTOC.xml | 6 ++- help/help/html/features/importvcf.html | 74 ++++++++++++++++++++++++++++++++ help/help/html/menus/alwfile.html | 9 ++-- 4 files changed, 83 insertions(+), 8 deletions(-) create mode 100755 help/help/html/features/importvcf.html 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 -- 1.7.10.2