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Cecilia Kardum Hjort

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Latest activity by Cecilia Kardum Hjort
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    Cecilia Kardum Hjort commented,

    1. Community
    2. Germline
    3. Sortvcf generated empty file. GATK4

    I apologize, I copied the wrong scripts. This was the initial command line that I tried to run and got an error message: java -Xmx32G -jar $PICARD_HOME/picard.jar SortVcf \I=SelectedINDELS_final.vc...

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    Cecilia Kardum Hjort commented,

    1. Community
    2. Germline
    3. Sortvcf generated empty file. GATK4

    danilovkiri, I sorted out the problem! I used GATK in the command line instad of PICARD and that seemed to work.  So this command: java -jar $GATK_HOME/gatk-package-4.1.4.1-local.jar MergeVcfs inst...

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    Cecilia Kardum Hjort commented,

    1. Community
    2. Germline
    3. Sortvcf generated empty file. GATK4

    the command gave me nothing (no error, but it ran for a bit but no output) gunzip -c -d FILENAME | grep -v "^#" | grep "3927,07"

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    Cecilia Kardum Hjort commented,

    1. Community
    2. Germline
    3. Sortvcf generated empty file. GATK4

    Where do I add the name of the file in the command line?

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    Cecilia Kardum Hjort commented,

    1. Community
    2. Germline
    3. Sortvcf generated empty file. GATK4

    Hi, danilovkiri Okey, that's strange. I'm new to this so I'm sorry for not knowing how to provide you with the header and some of the body lines in a proper way.  

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    Cecilia Kardum Hjort created a post,

    Sortvcf generated empty file. GATK4

    1. Community
    2. Germline

    Hi, I have two vcf files, one of filtered snps and one of filtered indels. I wanted to merge them with Mergevcf but received the error message: "Exception in thread "main" java.lang.IllegalStateExc...

    • Cecilia Kardum Hjort
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    • 13 comments
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    Cecilia Kardum Hjort created a post,

    Error message VariantFiltration GATK 4.1.4.1

    1. Community
    2. Germline

    Hi, I'm running VariantFiltration on a VCF (samples_combined.vcf) file that consist of two merged VCF files that I generated from SelectVariants (vcf files for SNPs and  INDELS separately); raw_snp...

    • Cecilia Kardum Hjort
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    Cecilia Kardum Hjort commented,

    1. Community
    2. Non-Human
    3. Speeding up GenotypeGVCFS? GATK4

    David Benjamin Thank for your reply! Could I run only the GenomcisGVCF with the -L option because the GenomicsDB has already been created? 

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    Cecilia Kardum Hjort created a post,

    Speeding up GenotypeGVCFS? GATK4

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    1. Community
    2. Non-Human

    I'm currently in the process of creating my own dataset of known variants, since one doesn't exist generated from WGS for my study species (bumblebee). However, the step of performing joint genotyp...

    • Cecilia Kardum Hjort
    • 7 followers
    • 17 comments
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