Follow @OpenCravat
Help
|
Release notes
|
How to Cite
|
Contact
|
Log-in
Username:
Password:
Forgot username?
Forgot password?
Create an account
|
My Jobs
|
My Profile
Set timezone
Change password
Change password challenge
|
Setup
|
Server Status
|
Log-out
Password change successful
Retrieve Username
Username is your email address.
Reset Password
Username:
Get challenge question
Question:
Answer:
Submit
Change Password Challenge Question/Answer
Question:
Answer:
Submit
Create an Account
Your email (will be your username):
Password:
Retype Password:
Submit
Set Timezone
Current timezone:
Choose timezone:
Submit
Change Password
Username:
Current password:
New password:
Retype new password:
Submit
CRAVAT v4.3
July 5, 2016
Released Dockerized CRAVAT (
here
).
Reduced installation space requirement from 500GB to 200GB
Added CRAVAT Setup page.
Improved Interactive Result Page, which includes:
- Summary-level result with charts and Circos plot
- Error tab
- Variant-level result for transcript-coordinate input
Added ClinVar and ClinGen annotation.
Timezone and security question and answer have been added to user information.
ESP6500 database has been updated to V2-SSA137.
Improved UI.
Fixed bugs.
CRAVAT v4.2
December 29, 2015
Added protein domain annotation from Pfam on the Interactive Result Page.
Various minor bug fixes
CRAVAT v4.1
December 1, 2015
Added
VEST-indel for annotating pathogenicity of indels.
Added Interactive Result Page, which includes:
- Variant- and gene-level results
- Filtering by CHASM and VEST p-values as well as allele frequency
- Multiple-column sorting
- Text search for selected columns
- Showing/hiding result table columns
- Lollipop diagram of input mutations over gene, with protein domain/site and TCGA mutations
- Embedded MuPIT Interactive
Updated Job List Page, which includes:
- "Explore" button to open Interactive Result Page
Added gene-level CHASM cancer driver composite p-value and FDR
Added CHASM and VEST scores and p-values to all the transcripts each input mutation maps to.
Deleted "Codon Level" tab from the result spreadsheet.
Fixed bugs.
CRAVAT v3.2
May 12, 2015
Added RESTful API for annotating a single mutation.
Added analytical p-values for VEST pathogenicity scores for non-silent mutations.
Added gene-level p-value and FDR for VEST pathogenicity score based on Stouffer's Z-score method
Added indel scores.
Added mutation allele frequencies from
Exome Aggregation Consortium (ExAC)
release 0.3.
Added input line number to the report.
Added a report tab for non-coding mutations.
Added a report tab for errorneous input lines.
Removed the Codon Level report tab.
CRAVAT can now show both driver (CHASM) and pathogenicity (VEST) scores at the same time.
Updated VCF support (sequencing quality metrics, zygosity, and pileup coverage and allele frequency).
Updated
1000 genomes
annotation with Phase3 sequence freeze 20130502 (Includes chromosome Y variants).
Updated
ESP6500
annotation with version v0.0.30 (Includes chromosome Y variants).
Updated
GeneCards
summary annotation.
Updated MuPIT link out according to the new release of
MuPIT Interactive
.
Improved report layout.
Improved speed with pre-computation of VEST scores for all possible exome mutations.
Fixed bugs.
CRAVAT v3.1
July 18, 2014
Added
user account feature
(login/logout/password retrieval/change password and My Jobs page)
Added indel support for
dbSNP
and
ESP56500
annotation
Added
MuPIT
lookup and link out
Added
VCF input format
support
Added a
new, simpler indel input format
(no need to figure out the upstream base of an indel. Old format is still supported.)
Added
TARGET drug association DB
annotation
Added oncogene/tumor suppressor gene annotation (from the oncogene/TSG list by
Vogelstein et al.
)
CRAVAT v3.0
March 4, 2014
Updated with
CHASM 3.0, SNVBox 3.0, and VEST 3.0
Updated with COSMIC v68.
Added RESTful web service functionality. For more information, see
here
Added
Sequence Ontology annotation.
Added
mappability
annotation (UCSC 75 mer-alignability and blacklist tables).
Added indel support (Sequence Ontology and (for genomic-coordinate mutations only) COSMIC annotation).
CRAVAT v2.0
September 23, 2013
Updated with CHASM 1.0.8, SNVBox 2.0.0, and VEST 1.1.0
Updated with the classifiers for CHASM analysis
CRAVAT v1.0
November 13, 2012
Updated with the classifier and null distribution for VEST.
CRAVAT v0.5
August 30, 2012
Added a queuing system for multiple concurrent jobs.
Added a server status page.
Added ESP6500 allele frequencies.
Added MuPIT Interactive input file preparation option.
Added estimated run-time displayed after submission.
Fixed minor bugs.
Contact CRAVAT Team
Your email:
Message:
Check for VCF-format input example.
Check for CRAVAT-format input example.
Enter variants below:
Two input formats are supported: CRAVAT format and VCF format.
VCF format
See
VCF specification
for details.
CRAVAT format
See
input format help
for details.
Genomic-coordinate input format
UID, chromosome, position (1-based), strand, reference base(s), alternate base(s), and (optional) sample ID, separated by a space or tab. UID should not contain commas. For indels, use the following format. "-" means no base. Examples are below.
VAR1 chr22 25115449 + A G Sample1 (substitution)
VAR2 chr22 25115449 + - GA Sample2 (insertion)
VAR3 chr22 25115449 + GCA - Sample3 (deletion)
Transcript-coordinate input format
Variant ID, transcript identifier, amino-acid substitution, and (optional) sample ID, separated by a space or tab. An example is below.
VAR4 NP_001135977 R641W 1 (substitution)
or upload a variant file:
Two input formats are supported: CRAVAT format and VCF format.
VCF format
See
VCF specification
for details.
CRAVAT format
See
input format help
for details.
Genomic-coordinate input format
UID, chromosome, position (1-based), strand, reference base(s), alternate base(s), and (optional) sample ID, separated by a space or tab. UID should not contain commas. For indels, use the following format. "-" means no base. Examples are below.
VAR1 chr22 25115449 + A G Sample1 (substitution)
VAR2 chr22 25115449 + - GA Sample2 (insertion)
VAR3 chr22 25115449 + GCA - Sample3 (deletion)
Transcript-coordinate input format
Variant ID, transcript identifier, amino-acid substitution, and (optional) sample ID, separated by a space or tab. An example is below.
VAR4 NP_001135977 R641W 1 (substitution)
Clear
hg18
If genomic-coordinates are used for variants,
they are assumed to be in hg19.
To use hg18 instead, check this box.
Send the analysis report
to:
An excel file where analysis results
are organized into tabs.
Include text reports
Additional tab-delimited text files for
easy programmatic processing
will also be included.
What will I get?
Query a single variant (chr_pos_strand_refbase_altbase):
