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  • Calling SNPs and InDels simultaneously or seperately?

    Hi,

    I want to know when call variants by GATK pipeline, you call SNPs and InDels simultaneously (use -glm BOTH) or separately in two rounds of run. I noticed that considering BAQ will decrease the performance of calling InDels. But how can I deal with the conflicted alleles generated by SNPs and their nearby InDels?

    Best,
    SK

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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.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

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