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Julianne Radford

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Latest activity by Julianne Radford
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    Julianne Radford created a post,

    Checking ReadGroup name in BAM file with GATK instructions

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    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: c) Entire error log: If not an error, choose a category for your question(REQUIRED):a)How do I (....

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    Julianne Radford created a post,

    HaplotypeCaller and Read Group Errors

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    GATK version used: 4.1.9.0 (1) trying to use HaplotypeCaller including "--java-options "Xmx4g" command.  Exact command used: (base) Juliannes-MacBook-Pro:gatk-4.1.9.0 julianneradford$ ./gatk --java...

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    Julianne Radford commented,

    1. Community
    2. Non-Human
    3. emit-ref-confidence error

    Hi Genevieve Brandt (she/her) Thank you so much for the feedback. First question: do I have to include this bit in my HaplotypeCaller code? Because I haven't been as it returns an error when I try ...

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    Julianne Radford commented,

    1. Community
    2. Non-Human
    3. "No positional argument is defined" Error in HaplotypeCaller

    Hi Genevieve Brandt (she/her) I fixed the issue. I had a space between "-" and the characters (i.e. R, I, O, ERC). By deleting the space this resolved that problem.

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    Julianne Radford commented,

    1. Community
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    3. emit-ref-confidence error

    Hi Florence Morel,  Did you ever get an answer to this question: "Where can I find the sample name and how should I write the command line with the --sample-name argument?" I am having the same iss...

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    Julianne Radford commented,

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    3. HaplotypeCaller complains (in 2 different ways) about sample-name

    Hi there,  Naveen Eugene Louis, I am new to Linux / GATK, and have the same initial error as Terry Jones, and I am just wondering where exactly do you put this syntax: @RG\tID:XXX\tSM:XXX_sample? H...

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    Julianne Radford commented,

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    2. Non-Human
    3. "No positional argument is defined" Error in HaplotypeCaller

    Hi Genevieve Brandt (she/her) Yes thank you for replying. Here is the stack trace:  org.broadinstitute.barclay.argparser.CommandLineException$BadArgumentValue: Illegal argument value: Positional ar...

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    Julianne Radford created a post,

    "No positional argument is defined" Error in HaplotypeCaller

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    2. Non-Human

    Hi there,  I am trying to run HaplotypeCaller on some bam files, using this command: ./gatk HaplotypeCaller \ - R Rflav_transcriptome_sequences.fa \ - I SRR5341585.bam \ - O 85variants.g.vcf \ - ER...

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