Is VAI limited to 100,000 variants? Is there a way to run it on 4.5M variants?
open-cravat can handle unlimited number of variants. It can consume VCF format input files and produce tab-separated text output files as well as excel spreadsheets. It has visualization components which is still being polished but its command-line portion is quite solid. It is modular and open-source, and it is easy to write input and output format converters and custom report generators (you write only minimum specific parts since heavy lifting is done by open-cravat) or any annotation module for that matter. You can publish your converters, report generators, annotation modules, gene mappers, and etc with one command to cravat store for other people to install and use with one command or one click. It is Python based and installed with pip. Disclosure: I am the lead architect of open-cravat.
Sorry, I just now noticed that the question was from years ago.
When referring to a package it is customary to include links. Multiple packages can have similar names. I think you are referring to this package?
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version 2.3.6
Looks interesting, although I am always very irritated when tools like this are seemingly released only as web-based tools. I'm much less apt to actually use them when that is the case
I also have not used VAI yet, but agree with @Dan -- our group moved away from SeattleSeq annotation (and its web portal) to Annovar (local install) due to the lag time of SSeq and restriction on number of jobs you could run per IP address. Nothing like having that local install for annotation.
Agreed. Although I have moved to snpEff + GEMINI over Annovar. Annovar was just too cumbersome and I prefer working with VCF files for as much of the workflow as possible.
I like the advantage of GEMINI as well. Moreover, GEMINI is MIT license and ANNOVAR is just not really opensource. What do you think?
Well Annovar now handled input VCF and will output to VCF as well. Theoretically it would not be possible to write a parser to get Annovar annotated VCF files into GEMINI. I don't see the two as competing. While GEMINI does add extra annotations it is layered on top of the annotations you already obtain by using snpEff or VEP currently.
I don't mind that Annovar isn't open source. They obviously had plans for commercial support and licensing and with the launch of Tute Genomics I think they have finally gotten there. Meanwhile they still support a free to use (and valuable) tool for the research community.
i have tried it, feed it with a merged vcf file produced by GATK as input, but unfortunately, it says that the vcf file format is wrong, can not figure out why that happens and returned to use annovar again.