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GermlineCNVCaller parameters for targeted sequencing

Hi all,

I am testing the presence of CNVs on target sequencing data related to a gene panel of ~100 genes. I have seen in the forum and from various posts that some of the parameters changes between WGS and WES. What about a small target sequencing study? Do you have any recommended set of parameters to be used?

Thanks in advance

Best Answer


  • bshifawbshifaw Member, Broadie, Moderator admin

    Hi @Nspataro ,

    You should be able to find any recommended parameter changes in either the Tool Documentation or the (How to) Call common and rare germline copy number variants tutorials.

  • NspataroNspataro Member
    Actually, I did not find any recommendation in the suggested pages. Moreover, I had a quite extensive look at many entries of the forum and I did not get any clear conclusion. By the moment I am using a setting that was suggested for WES experiments. Apparently, we get nice results but we need to further validation. Please come back to this post if you get any update related to gene panel sequencing
  • NspataroNspataro Member
    Thank you very much for the quick answer. Just a comment for the rest of the users: our results indicates that even if using WES parameters the GermlineCNVCaller performs better than XHMM on the Truesight hereditary cancer panel.
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