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lid.zigh

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Latest activity by lid.zigh
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    lid.zigh commented,

    1. Technical Documentation
    2. Glossary
    3. VCF - Variant Call Format

    Hello,  I have the same question too. "If it is not advised to combine VCFs for multiple samples, what would be the recommended method to compare variants in separate VCFs for multiple samples afte...

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    lid.zigh commented,

    1. Community
    2. Other
    3. MarkduplicatesSpark failed

    Hello Genevieve, Thank you for your kind help. I will try my script with system tmp folder instead of my tmp folder and hope it solves the issue. I will keep you updated. Thank you, Lida  

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    lid.zigh created a post,

    MarkduplicatesSpark failed

    Answered
    1. Community
    2. Other

    Hello , I have been running MarkDuplicatesSpark on one Sam file to get bam file and after couple of hours running it failed.  Could you please help me to figure out what the issue is. Thank you GAT...

    • lid.zigh
    • 3 followers
    • 5 comments
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    lid.zigh commented,

    1. Announcements
    2. Blog
    3. Welcome to the new home of GATK

    Hello Geraldine Van der Auwera, I just started working with GATK4 and was looking for new version of RealignerTargetCreator and IndelRealigner and notice this post. Could you please confirm that no...

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    lid.zigh created a post,

    calling large scale structural variants

    Answered
    1. Community
    2. Special GATK Use Cases

    a)How do I call large scale structural variants using GATK version 4.2 and which command line I need to use?  Thank you, Lida 

    • lid.zigh
    • 2 followers
    • 1 comment
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