Tool:CRAVAT: a web tool to annotate and analyze cancer variants
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6.3 years ago
Collin ▴ 980

CRAVAT provides high-throughput services for researchers to annotate and prioritize small-scale exome variants and genes discovered in normal tissues and cancers. Annotations include TARGET drug associations, 1000 Genomes, Exome Variant Server and Exome Aggregation Consortium (ExAC) minor allele frequencies by population.  Variant zygosity, pileup coverage and variant allele frequencies are provided when users submit vcf files.  Cancer-specific annotations include COSMIC mutation frequencies by tumor type, Vogelstein/Kinzler oncogene/tumor suppessor gene assignments and PubMed hits. Variant- and gene-level annotations and bioinformatic scores are provided to enable interpretation and prioritization of variants identified in sequencing studies, including frameshift and in-frame insertions/deletions, splice site, missense and nonsense. Variants can be submitted either as a Variant Call File (vcf) or in a simple tab-delimited format, based on genome coordinates, by uploading through a graphical web interface or a RESTful web services API.

We have now released CRAVAT 4.0 Beta with a new interactive interface, sortable tabular views of results in worksheet format are enhanced with graphical displays that highlight significant properties of variants and genes, including protein-domain based lollipop displays and viewing variants on annotated human 3D protein structures and theoretical homology models.  For users interested in cancers, TCGA mutations from 31 cancer types in 1D and 3D, and statistically significant 3D mutation clusters can be viewed for each cancer type and for TCGA's Pan-cancer study of 12 tumor types.

You can find CRAVAT at http://www.cravat.us/, and additional help information at http://www.cravat.us/help.jsp. To beta test the new interactive viewer to explore exome variants in more depth, please contact the CRAVAT team by email at support@cravat.us.

sequencing Cancer annotation variant Tool • 4.8k views
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What is the size limit of VCF file that I can upload to CRAVAT? Can I upload compressed VCF file?

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23 months ago
slcrick ▴ 250

There is currently no limit for VCF files on cravat.us. Only uncompressed VCF files are supported.

By the way, there is a new evolved version of CRAVAT. Check out OpenCRAVAT at run.opencravat.org (Web server) and https://github.com/KarchinLab/open-cravat/wiki (stand-alone version).

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Hi! Thanks for the realy nice tool, could you, please clarify coiuple of questions:

1) How can I launch CRAVAT on several cores on a server? I did not found any buildin options for that 2) I experience following problem: I'm running cravat on remote server (which works fine) and then want to analyse output on my local machine via SHH tunel. I've managed to launch python server on the remote machine with "oc gui out.sqlite" comand, and open cravat in my browser on local machne. Newertheless, I do not see the processed file in gui -- the interface is empty. I'm not sure what is the problem and is it possible to solve it?

update, for someone, how might be looking for this: https://github.com/KarchinLab/open-cravat/issues/17

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