Tool: CuteVariant : A GUI to filter VCF file
Hi,
Let me show you my new application in development: CuteVariant.
This a Qt C++/GUI application to filter and display VCF file.
Actually this is an alpha preview. I didn't publish any release but the source code is avaible.
If you know snpSift and variant-tools, I mixed features comming from both.
Feature:
- Load raw VCF or annotated VCF file ( tested with snpSift and VEP )
- Parse the VCF file and save datas into SQLITE database
- Select annotation and genotype columns datas
- Filter with a condition tree
- Store Views
- Sort & group variants ( by transcript .. )
- Type your own query using a "variant query language" ( looks like sql / snpSift export)
Next Feature comming soon :
- Set operation (child - (father & mother))
- Open variant with custom http query ( IGV, varsome, UCSC ... )
- Statistics charts
- And many more ...
Feel free to suggest any ideas.
You can find the code on github
You can talk with us on gitter
Video preview on Youtube ==> https://youtu.be/h8sSQa-WSmI
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richardcaseyhpc •
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sacha
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sacha
1 answer
Alpha release 0.1 avaible for Linux as AppImage.
wget https://github.com/labsquare/CuteVariant/releases/download/untagged-7a62372818b54b6974df/CuteVariant-0.1-x86_64.AppImage
chmod +x CuteVariant-0.1-x86_64.AppImage
./CuteVariant-0.1-x86_64.AppImage
You can import *.VCF file annotated with SnpEff/VEP.
This alpha version contains bugs and have missing features.
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Can I ask which platform you want to support? win, mac or linux?
All of them. It's Qt5 based.
Any idea on the maximum number of SNPs this has been tested with ? Eg 2-10m SNVs from WGS data would be of interest to my users.
I only tested with exom for now . But It should works with WGS if you computer has sufficient disk memory.
Hello, Does your tool work with variants from non-model organisms like the dog? Thanks.
It should works for all kind of vcf
Hi, I would suggest using Docker or Singularity containers to distribute the application. Very easy for end users.