Avatar

Chadi Saad

  • Total activity 9
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 1
  • Subscriptions 3

Activity overview

Latest activity by Chadi Saad
  • Avatar

    Chadi Saad commented,

    Hi Yossi, To use "CheckFingerprint", do we need to build the HAPLOTYPE_MAP from our population ? we have a multisample VCF (not phased) containing thousands of samples. Or it's ok to use the public...

  • Avatar

    Chadi Saad commented,

    Hi Genevieve-Brandt-she-her Thanks for your reply. Actually my comment was about tools like Indel-realigner, VarQual recalibrator. Not about annotation. Is it possible to run this tools using a new...

  • Avatar

    Chadi Saad created a post,

    dbSNP version for GATK best practices pipeline

    The GATK data resources bundle for gatk best practices contains dbsnp ver 138. Is it possible to use an updated version (like v151) for bqsr & vqsr ? or it is recommended to use the same version as...

  • Avatar

    Chadi Saad commented,

    So If I 'm not using, neither Matched Normal nor PoN nor Population ressources, there is no reason for Mutect2 to miss germline variants. Do you agree ? Thanks

  • Avatar

    Chadi Saad created a post,

    Call germline mutations from Mutect2

    Is it possible to call germline mutations with Mutect2 (in addition to somatic variants) ? Because I read on the net, that the algorithm of Mutect2 will eliminate germline variants and I have to us...