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Haiying Kong

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  • GATK Funcotator missing DP and AF information from vcf file

    1. Community
    2. Somatic

    I am running Funcotator in gatk-4.1.9.0 to annotate vcf files. gatk Funcotator \-R $hg -V ${Lock_VarDict_dir}/$sample.vcf -O ${Result_VarDict_dir}/$sample.maf \--output-file-format MAF --ref-versio...

    • Haiying Kong
    • 2 followers
    • 3 comments
    • 0 votes

  • GATK Funcotator Variant_Classification

    1. Community
    2. Somatic

    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 (....

    • Haiying Kong
    • 2 followers
    • 1 comment
    • 0 votes

  • Funcotator missing AF

    1. Community
    2. Other

    I am using Funcotator on GATK4. I found the the following particular variant in vcf file has missing AF value in the maf file produced by Funcotator. 2113 variants out of 1032388 total variants are...

    • Haiying Kong
    • 2 followers
    • 1 comment
    • 0 votes

  • Any documents for 199 columns in Funcotator output?

    1. Community
    2. Other

    GATK version 4 Funcotator  I got 199 columns in output. Is there any document to explain these columns?

    • Haiying Kong
    • 2 followers
    • 2 comments
    • 0 votes