Regarding Different genotypes for same sample using Unified Genotyper & Haplotype Caller

tahseentahseen IGIB,New DelhiMember

Hello Team,

I am doing multi sample cohort exome analysis for which i have called SNPs using both callers (UG & HC).For one of my important SNP, i am observing different genotypes in few samples from both the callers.
Which to rely upon for further analysis???

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @tahseen

    Would you please give us some more information.
    Version of GATK you are using? The exact command you are using?
    Would you please post records of the SNP you mentioned. Thank you!

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    We haven't heard from the user in more than two business days. The user has been notified and this ticket is now closed.

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