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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


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by Sheila

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  • 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 ✭✭✭✭✭

    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.


  • 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 !

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