Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

CNView: new software for plotting CNVs

Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

I came across this rather tantalising program for plotting multi-sample CNVs in genomic intervals. It requires depth data in bed format. This might require bed tools.

I was wondering if you could direct me to a genomestrip file that contains the depth information.

I was thinking it might be profile_seq_chr4_100000.dat.gz (from preprocessing), or *.genotypes.counts.dat (from deletion discovery/genotyping).

The link to the software is:
https://github.com/RCollins13/CNView#cnview-summary

Best Answer

Answers

  • Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

    @RLCollins I haven't tried any of the above yet. Is it compatible with non-human organisms? I suspect a bit more tweaking is required.

Sign In or Register to comment.