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Jacob Wang

  • Total activity 24
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Activity overview

Latest activity by Jacob Wang
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    Jacob Wang commented,

    Hi, Genevieve Brandt (she/her) It's my pleasure to work with the GATK team and be able to contribute. I just ran the following steps (from merging gvcfs to annotation) using those gvcfs in the past...

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    Jacob Wang commented,

    Thanks, Pamela. I ran the following steps (from merging gvcfs to annotation) using the gvcfs in the past weekend. No problem happened. I think for now I can say the problem has been fixed. I will p...

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    Jacob Wang commented,

    Hi, Genevieve Brandt (she/her) I think I and Pamela Bretscher have solved the problem. I re-run both the steps of BQSR and HaplotypeCaller with the --use-jdk-inflater or --use-jdk-deflater option...

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    Jacob Wang commented,

    Hi, Pamela!      Good news! I think we have solved the problem. I re-run for the two individuals both of the steps of BQSR and HaplotypeCaller with the --use-jdk-inflater or --use-jdk-deflater opti...

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    Jacob Wang commented,

    Hi Pamela Bretscher, I have run the two commands on my bam files as you suggested. I kept the intermediate bam files (after steps 3.Alignment, 4.Fixmate, 5.Sorting, 6.Deduplication and 9.BQSR) so I...

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    Jacob Wang commented,

    Hi Pamela,     Thank you for the suggestion. I have run PrintBGZFBlockInformation for the .bam files (after the step of BQSR) of the three samples with the default parameters. The files generated b...

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    Jacob Wang commented,

    Hi  Genevieve Brandt (she/her)     Thank you all the same. I hope it could be solved in the future version.

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    Jacob Wang commented,

    Hi Pamela, Thank you for your reply! I will try PrintBGZFBlockInformation as you suggested. I noticed from its help doc that PrintBGZFBlockInformation itself has parameters: --use-jdk-deflater & --...

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    Jacob Wang commented,

    Hi Genevieve Brandt (she/her)     I encountered the same error when using HaplotypeCaller. As Pamela Bretscher suggested I tried using those two options but it seemed that it didn't work in my cas...

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    Jacob Wang commented,

    Hi Pamela Bretscher ,      Could you give me any other suggestions? I can provide any other information to solve this bug? Does this error only been reported after GATK 4.0?      Thank you very muc...