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Unified genotyper and Haplotype Caller for exome sequencing data

lalirlalir CanadaMember

Hello everyone,
I have recently sequenced 15 sample exomes using the Ion proton system, which directly generates VCFs after sequencing runs. However, since I will be using GATK for downstream analysis, I have decided to recall the variants using UG or HC. I read a document stating that HC should not be used in the case of pooled samples. Can someone clarify what exactly this means? For Ion proton, three samples are barcoded and pooled together prior to sequencing. Also, is 15 samples enough to obtain good discovery power? I was thinking of using external, publicly available bam files of exome sequencing data if 15 samples is not sufficient for joint variant calling.

Thanks in advance,


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Ricky,

    When we say pooled samples we mean samples that are not barcoded before being mixed. If your samples are barcoded it's fine, you can use the HC.

    The more samples, the better, especially for VQSR filtering. If there are available exomes that match your population, then it may be helpful to use them.

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