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CRAVAT v5.2.4
October 29, 2018

Added denovo-db annotation to MuPIT Interactive.
Improved the layout of CRAVAT Single Variant page.
Fixed minor bugs with VCF format input in CRAVAT.
Fixed minor bugs with CRAVAT Single Variant page.
Fixed minor bugs in CRAVAT and MuPIT Interactive.

CRAVAT v5.2.3
June 8, 2018

Added homology models for UniProt protein sequences to MuPIT Interactive.
Fixed image capture in MuPIT Interactive.
Added a homology model of BRCA2 to MuPIT Interactive.
Fixed minor bugs.

CRAVAT v5.2.2
April 20, 2018

Improved setup with checksum and smaller download chunks.
Improved the contact form.
Implemented approximate matches for indels in 1000 Genomes annotation.
Fixed minor bugs.

CRAVAT v5.2.1
Febuary 1, 2018

Increased coverage of RefSeq transcripts.
Added a CRAVAT single variant annotation page that can be linked to externally.
Added custom annotations to MuPIT for integration with BRCA Exchange.
Added two BRCA Exchange data tracks to MuPIT: Tavtigian Priors and Multifactorial Model

CRAVAT v5.2.0
January 3, 2018

GnomAD replaced ExAC.
Version numbers are not needed for transcript-coordinate input format.
Improved performance for GeneCards and PubMed annotation.

CRAVAT v5.1.1
November 28, 2017

All mutated genes correctly displayed in NDEx diagrams.
Variants on gene tab lollipop diagram increase in height based on the number of occurrences of the variant in the submitted cohort.
Fixed OMIM linkout on gene tab.

CRAVAT v5.1.0
November 2, 2017

Added extensive noncoding annotations including:

UTRs, introns, and upstream/downstream regions of a gene.
Noncoding RNAs.
Repetitive sequences.
Pseudogenes
GRASP-GWAS

Other Bug fixes and improvements

CRAVAT v5.0.2
September 30, 2017

Fixed VCF conversion failure.
Fixed MuPIT mapping (protein alignment rebuild).
Fixed "Hide Synonymous" filter in the Interactive Result Viewer.
Fixed issues related to MuPIT pop-up in the Interaction Result Viewer.
Improved Help page.
Other Bug fixes and improvements

CRAVAT v5.0.1
August 30, 2017

Minor bug fixes and improvements

CRAVAT v5.0.0
May 17, 2017

CRAVAT/MuPIT has been built on GRCh38.
- CRAVAT 5
- MuPIT 5
- SNVBox 5
Single variant annotation page has been added.
Load control panel has been added, with which a job with more than 100,000 variants can be trimmed down and examined on CRAVAT Result Viewer.
VEST null distribution has been improved with Gibbs sampler.
ExAC database has been updated to v1.0
ClinVar database has been updated to v1.46
Cosmic database has been updated to v80.
dbSNP database has been updated to v147.
UniProt database has been update to Release 2017_05.

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 us with questions or issues: support@cravat.us

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