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Varun Gupta

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Latest activity by Varun Gupta
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    Varun Gupta created a post,

    --max-events-in-region in FilterMutectCalls

    1. Community
    2. General Discussion

    REQUIRED for all errors and issues: a) GATK version used: 4.1.5b) Exact command used: N/Ac) Entire program log: N/A Hello, What is the explanation of --max-events-in-region parameter from FilterMut...

    • Varun Gupta
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    Varun Gupta created a post,

    Somatic mutations detection using mutect2

    1. Community
    2. Somatic

    REQUIRED for all errors and issues: a) GATK version used: 4.1.5b) Exact command used: See belowc) Entire program log:    Hello Gatk team, I ran mutect2 on tumor bam file and normal bam file separat...

    • Varun Gupta
    • 1 follower
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    Varun Gupta created a post,

    vcf files for BQSR step

    Answered
    1. Community
    2. Documentation Questions

    Hi, I am using gatk4 BaseRecalibrator command and I need a known vcf file to input for --known-sites argument. Where can I download the vcf file? GATK is installed on our cluster and I have read th...

    • Varun Gupta
    • 7 followers
    • 4 comments
    • 1 vote