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Rafael Viana

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Latest activity by Rafael Viana
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    Rafael Viana commented,

    1. Getting Started
    2. Tutorials
    3. (Notebook) Intro to using Mutect2 for somatic data

    Very nice article.I just have 2 questions.1- Once you filter your variants and have the PASS flag.    Is there a tool to remove the ones without the PASS flag? 2- Here you get the differences betwe...

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    Rafael Viana commented,

    1. Community
    2. Somatic
    3. Created panel of normals returns empty vcf

    Hi Genevieve,Thank you for the response. To produce the exome we used commercial kits (Agilent Sure select v6).Reads were mapped to Homo Sapiens GRCh38p13.rel102.dna.primary_assembly.Qualimap finds...

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    Rafael Viana created a post,

    Created panel of normals returns empty vcf

    Answered
    1. Community
    2. Somatic

    Hi I am trying to make my own panel of normals for human exome using gatk v4.1.9.0 (installed with conda).I am using a version of the genome where chromosomes are written just with the number (with...

    • Rafael Viana
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