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  • hr3y
    started a topic GATK HaplotypeCaller READS?

    GATK HaplotypeCaller READS?

    Hi everyone, I was wondering if anyone knows exactly how does GATK HaplotypeCaller treat unmapped reads.

    The thing is, first GATK defines <<active regions>> in which it will operate, after this, it goes one by one and builds an assembly graph using the reference sequence. Once it has the graph, it "takes each read in turn and attempts to match it to a segment of the graph; whenever portions....".

    The question is, when it takes EACH READ in turn, it means, the reads that mapped there, right? not every single read in the bam file.

    Is there anyone who knows the excplicit answer?

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  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

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    02-08-2024, 06:33 AM

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