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Lucas Kopecky Bobadilla

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Latest activity by Lucas Kopecky Bobadilla
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    Lucas Kopecky Bobadilla commented,

    1. Community
    2. Somatic
    3. AnalyzeCovariates

    I actually figure it out by running the R script alone. It seems that it is needed to transform the csv file strings to factor.   By adding changing the line 16 from: data <- read.csv(args[1]) to d...

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    Lucas Kopecky Bobadilla created a post,

    AnalyzeCovariates

    1. Community
    2. Somatic

      Hello I am using the current 4.17 GATK version and I am trying to run AnalyzeCovariates. I ran the baserecalibrator to get the table file to run AnalyzeCovariates but I am getting this following ...

    • Lucas Kopecky Bobadilla
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    Lucas Kopecky Bobadilla created a post,

    mergeBam picard issue

    1. Community
    2. Germline

    Hello,    I'm having issues with the mergeBam function from Picard. I getting the following error: Exception in thread "main" java.lang.IllegalStateException: Aligned record iterator (A00419:256:HK...

    • Lucas Kopecky Bobadilla
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    Lucas Kopecky Bobadilla created a post,

    RNA-seq - VCF file BQSR non-model organism

    1. Community
    2. Other

      Hello,  I am currently working with a non-model plant RNA-seq dataset for variant discovery. I started to follow the pipeline in the GATK website, but I got stuck at the BQSR step. I have an asse...

    • Lucas Kopecky Bobadilla
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