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Ran Wei

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Activity overview

Latest activity by Ran Wei
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    Ran Wei created a post,

    Pileup output of GATK4 vs. GATK3

    Answered
    1. Community
    2. New User Advice

    Hello, I am updating our workflow from GATK3.x to GATK4.x. The current protocol depends on the refined bam files generated ("This app outputs the refined (deduplicated, realigned, and recalibrated)...

    • Ran Wei
    • 2 followers
    • 1 comment
    • 0 votes
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    Ran Wei commented,

    1. Community
    2. New User Advice
    3. Empty intersection error when applying intervals

    Thank you Genevieve. However, when I change -isr to UNION, it seems that the GATK will map the variants to the whole genome, which does not fit my goal of setting the intervals - save running time....

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    Ran Wei created a post,

    Empty intersection error when applying intervals

    Answered
    1. Community
    2. New User Advice

    Hi, I am a first-time user of GATK. I am using the GATK4 haplotypecaller (parallel per-intervalbyns) version 2.0.1 embedded in the DNAnexus platform for variant calling. Several short intervals are...

    • Ran Wei
    • 4 followers
    • 8 comments
    • 0 votes