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jingchun liu

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Latest activity by jingchun liu
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    jingchun liu created a post,

    BQSR and VQSR resource sequences

    1. Community
    2. Germline

    Hi, When I am trying to do the BQSR and VQSR, both has  the same error message: The commands for BQSR: java -jar $gatk BaseRecalibrator \-R ./Homo_sapiens_assembly38.fasta \-I ./germline_analysis/g...

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    jingchun liu commented,

    1. Community
    2. Germline
    3. selectvariants error when consolidating GVCFs

    Pamela, Thank you so much! I thought gendb:// is just to tell the directory of the file. Now I know it tells gatk the file format and directory both. Kind regards, Jingchun

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    jingchun liu created a post,

    selectvariants error when consolidating GVCFs

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    1. Community
    2. Germline

    Hi, GATK4.2.2.0. is being used. I am trying to follow the book genomics in the cloud. Create variants GVCF file for mom, father and son. First combine mom and father's GVCF files and select variant...

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