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Huma Shehwana

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Latest activity by Huma Shehwana
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    Huma Shehwana created a post,

    Baserecalibarator error: half of the files worked without any error

    Answered
    1. Community
    2. Somatic

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.3b) Exact command used: gatk BaseRecalibratorSpark -R /DATA/peeper_lab/reference_fasta_files/GRCh38.d1.vd1.fa -I PRA...

    • Huma Shehwana
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    Huma Shehwana created a post,

    GATK ApplyBQSR error

    Answered
    1. Community
    2. General Discussion

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.3.0b) Exact command used: gatk ApplyBQSRSpark -R /DATA/peeper_lab/reference_fasta_files/GRCh38.d1.vd1.fa -I PRADO_da...

    • Huma Shehwana
    • 2 followers
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    Huma Shehwana commented,

    1. Community
    2. General Discussion
    3. GenomicDBimport error

    Thanks for looking in to it. I did try using the suggestions you gave however no luck. Here is my command and the subsequent log messages.  gatk  GenomicsDBImport --java-options "-Xmx32G" -R /DATA/...

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    Huma Shehwana commented,

    1. Community
    2. General Discussion
    3. GenomicDBimport error

    Hi Genevieve No, That is it. nothing after that.

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    Huma Shehwana created a post,

    GenomicDBimport error

    Answered
    1. Community
    2. General Discussion

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.3b) Exact command used: java -jar  /home/h.shehwana/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar  GenomicsDBImport -R...

    • Huma Shehwana
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    • 5 comments
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