Tool: CuteVariant : A GUI to filter VCF file
gravatar for sacha
11 days ago by
sacha810 wrote:


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.


  • 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 ==>

cutevariant preview

tool qt gui annotation vcf • 141 views
ADD COMMENTlink modified 11 days ago • written 11 days ago by sacha810

Can I ask which platform you want to support? win, mac or linux?

ADD REPLYlink written 11 days ago by Chen560

All of them. It's Qt5 based.

ADD REPLYlink written 11 days ago by sacha810

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.

ADD REPLYlink written 7 days ago by colindaven290

I only tested with exom for now . But It should works with WGS if you computer has sufficient disk memory.

ADD REPLYlink written 6 days ago by sacha810
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