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Laurent MANCHON

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Latest activity by Laurent MANCHON
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    Laurent MANCHON commented,

    1. Community
    2. Special GATK Use Cases
    3. splice variants are missing from the Mutect2 output

    from Mutect2 vcf output: zcat HD_829_Mutect2.vcf.gz | grep "chr17" | grep "7669692"chr17   7669692 .       T       G       .       .       AS_SB_TABLE=340,402|25,36;DP=817;ECNT=1;MBQ=20,20;MFRL=236...

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    Laurent MANCHON created a post,

    splice variants are missing from the Mutect2 output

    1. Community
    2. Special GATK Use Cases

    REQUIRED for all errors and issues: a) GATK version used: gatk-4.2.6.1 b) Exact command used: gatk --java-options "-Xms128G -Xmx128G -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:ParallelGCThreads...

    • Laurent MANCHON
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    Laurent MANCHON created a post,

    How to recover a mutation from secondary alignment

    1. Community
    2. Somatic

    REQUIRED for all errors and issues: a) GATK version used: gatk-4.2.6.1b) Exact command used:  gatk --java-options "-Xms80G -Xmx80G -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:ParallelGCThreads=1...

    • Laurent MANCHON
    • 2 followers
    • 2 comments
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    Laurent MANCHON created a post,

    base recalibration

    1. Community
    2. General Discussion

    REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: gatk --java-options "-Xms64G -Xmx64G -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:Parallel...

    • Laurent MANCHON
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