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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Missing annotations in the output callset VCF Follow


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    V S


    I am running HaplotypeCaller (Version="") with the following options :

    --annotation StrandBiasBySample
    --annotation TandemRepeat
    --annotation BaseQuality

    I read the annotations in the output VCF files (the variants are annotated with the SB, RPA, RU, STR, and MBQ tags). HaplotypeCaller works perfectly.

    Then, I am running GenomicsDBImport (Version="") followed by GenotypeGVCFs (Version="").

    I notice all the 3 annotations (StrandBiasBySample, TandemRepeat and BaseQuality) are missing in the multi-sample gVCF output file (3 VCF files are merged).

    I don't get explanation about this issue yet and after exploring the GATK forum, I don't have a clue. I really would like to report the SB and MBQ tags in the final gVCF file.

    Thank you very much for your help,

    Best Regard,


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    V S

    Dear, do you have any feedback to share from my previous post ? Merci

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    Kaalindi Misra

    Hi V,

    You have posted your question on to the blog and not to the forum. So, you should repost this question in the forum to get an answer from the GATK community.


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