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Paulo Ricardo

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Latest activity by Paulo Ricardo
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    Paulo Ricardo created a post,

    Tumor-match mode doubt

    1. Community
    2. New User Advice

    REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: Can I have a command like this: My case is inbred mice -i Tumor.bam -i normal1.bam -i normal2...

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    Paulo Ricardo commented,

    1. Community
    2. New User Advice
    3. Base Quality Score Recalibration doubt

    Thank you very much for your help!

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    Paulo Ricardo commented,

    1. Community
    2. New User Advice
    3. Base Quality Score Recalibration doubt

    hi Gökalp Çelik And to detect the somatic variants, how do I perform bootstrapping? Do I first call the variants with haplotype caller or mutect2? Because I called with mutect2 and tried to perform...

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    Paulo Ricardo created a post,

    Base Quality Score Recalibration doubt

    1. Community
    2. New User Advice

    REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: I have 35 samples from different genotypes and some from different sequencing batches, so my ...

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    Paulo Ricardo created a post,

    CreateSomaticPanelOfNormals (BETA) workflow

    1. Community
    2. Special GATK Use Cases

    REQUIRED for all errors and issues: a) GATK version used: v.4.4.0b) Exact command used: srun apptainer exec $GATK gatk GenomicsDBImport -R /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/PauloM_Analysis/G...

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    Paulo Ricardo created a post,

    Tumour Match Mutect

    1. Community
    2. New User Advice

    I'm analyzing mouse samples, I have tumor and normal samples, all of them from different individual. I have 7 normal samples, some from different batches of sequencing, I thought of running each tu...

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    Paulo Ricardo commented,

    1. Community
    2. New User Advice
    3. Creating PON

    13:03:15.796 INFO  CreateSomaticPanelOfNormals - Initializing engine13:03:15.999 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/M>13:03:16....

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    Paulo Ricardo created a post,

    Creating PON

    1. Community
    2. New User Advice

    REQUIRED for all errors and issues: a) GATK version used: v.4.4.0I'm using your lates docker image, docker pull broadinstitute/gatk:latest That supposely has the function createsomaticPon, however ...

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    Paulo Ricardo commented,

    1. Community
    2. New User Advice
    3. Germline Variants Calling

    Could I apply funcotator to mouse samples? And which databases would I need?

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    Paulo Ricardo commented,

    1. Community
    2. New User Advice
    3. Germline Variants Calling

    And could I ask you, for annotating variants can I use snpEFF tool on the output of Mutect2? Or do you recommend GATK VariantAnnotator?