Tool: CuteVariant : A GUI to filter VCF file
gravatar for sacha
9 months ago by
sacha1.2k 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 • 573 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by sacha1.2k

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

ADD REPLYlink written 9 months ago by Chen670

All of them. It's Qt5 based.

ADD REPLYlink written 9 months ago by sacha1.2k

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 9 months ago by colindaven700

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

ADD REPLYlink written 9 months ago by sacha1.2k
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