Disclaimer
We assume no responsibility or liability for any loss or damage incurred as a result of any use of the information contained within or downloaded from this website.
If you have any problems, please let us know
Using custom cell lines
You can view a track showing the haplotype of a given cell line.
To use a custom cell line in the Genoverse browser, you must first enable it.
In the top-left corner of the Genoverse, open the "Tracks" menu and click select the
tracks you want to add from the list of available tracks.
Some cell lines may be hidden. If you don't see any available cell lines and you need access to them, please contact wge@sanger.ac.uk.
When you enable the tracks, they will appear at the bottom of the Genoverse browser.
You can move them where you want using the handle at the left on the browser.
Your preferred settings will still be there when you next use WGE
(this is saved in your web browser so will not be retained if you use WGE in a
different web browser or on a different computer).
You can delete tracks by expanding the track controls on the right of the track and
pressing the bin icon.
It is also possible to rearrange or delete tracks from the tracks menu.
Creating custom cell lines
Custom cell lines are supported from WGE v0.124 onwards.
To support custom cell lines, you will need a few special tables:
CREATE TABLE haplotype (
id SERIAL PRIMARY KEY NOT NULL,
species_id TEXT NOT NULL REFERENCES species(id),
name TEXT NOT NULL UNIQUE,
source TEXT NOT NULL,
restricted TEXT[]
);
CREATE TABLE user_haplotype (
user_id INTEGER NOT NULL REFERENCES users(id),
haplotype_id INTEGER NOT NULL REFERENCES haplotype(id)
);
For each cell line you want to add, you should also create a table of the form:
CREATE TABLE haplotype_<NAME> (
id SERIAL PRIMARY KEY,
chrom TEXT NOT NULL,
pos INTEGER NOT NULL,
ref TEXT NOT NULL,
alt TEXT NOT NULL,
qual NUMERIC,
filter TEXT,
genome_phasing TEXT
);
You should also add an entry to the haplotype table. The source column should contain the name of the specific haplotype table you added.
You can extract the information you need from a VCF file using the import_vcf.pl script. You can run it with the command:
import_vcf.pl --source <VCF file> --line <NAME>
This will create a CSV file named <NAME>.csv which can be imported into the haplotype_<NAME> table using the Postgres \COPY command.
Restricting access to cell lines
If a cell line is not supposed to be widely available, you can restrict access to it to certain users.
It is also possible to restrict access to specific chromosomes. The restricted column is
an array containing a list of restricted chromosomes. To restrict access to the Y chromosome
specifically:
UPDATE haplotype SET restricted='{"chrY"}' WHERE id=<ID>;
To restrict access to the X and Y chromosomes:
UPDATE haplotype SET restricted='{"chrX", "chrY"}' WHERE id=<ID>;
It can also be set to block everything (by giving it a value of *).
UPDATE haplotype SET restricted='{"*"}' WHERE id=<ID>;