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.

visualize CNV results from WGS analysis

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all, please would you advise :

what would be the best way to visualize the CNV that were predicted based on WHOLE-GENOME CANCER samples ?
shall we upload in IGV both BAM files for TUMOR and GERMLINE, although these files are pretty big (> 60-80 GB) ...
or possibly is there any other way ? thank you very much,

-- bogdan

Tagged:

Issue · Github
by Sheila

Issue Number
2870
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
sooheelee

Best Answer

Answers

  • BogdanBogdan Palo Alto, CAMember ✭✭

    And although I can upload the BAM files for TUMOR and GERMLINE in IGV, when I zoom-out in IGV, for some reason, the tracks can not be seen anymore .

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Bogdan
    Hi Bogdan,

    We are in the process of updating the Best Practices page for CNVs. If you check back there in a week or so, you should find more information, as the workflow has changed.

    -Sheila

  • BogdanBogdan Palo Alto, CAMember ✭✭

    Thanks a lot Sheila ! have a good weekend !

  • BogdanBogdan Palo Alto, CAMember ✭✭

    Dear Sheila, if I may add another question on the same topic please : for the visualization/verification of CNV areas in WGS data (cancer, germline), do we still still need the CN files (as described at
    https://software.broadinstitute.org/software/igv/CN) ? I would think that these CN files relate to SNP/CGH arrays and not to illumina sequencing kits ? thanks a lot, and have a wonderful weekend !

  • BogdanBogdan Palo Alto, CAMember ✭✭
    edited January 2018

    Thank you very much for a very comprehensive and detailed answer !

Sign In or Register to comment.