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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

GenomicsDBImport - why "intervals" is required??

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    Genevieve Brandt (she/her)

    Thank you for your post, Jianying Li! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

    Please see our Support Policy for more details about how we prioritize responding to questions. 

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    Jianying Li

    Thanks Genevieve! Here is the follow up question, in the help document the "intervel -L" is not required. But, when I issued for following command:gatk GenomicsDBImport -R  /ddn/gs1/home/li11/project2017/exomeSeq/SangerWG/GRCm38_68_ref/GRCm38_68.fa  --genomicsdb-workspace-path /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/testDir/PONtest/pon_db    -V
     /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/NormalSamples/MD6831b_output_raw_snps_indels.vcf.gz  -V /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/NormalSamples/MD6837b_output_raw_snps_indels
    .vcf.gz 

    It complains with the log like:

    A USER ERROR has occurred: No intervals specified

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    Genevieve Brandt (she/her)

    Hi Jianying Li,

    Please see the tool documentation for the detailed description of GenomicsDBImport. Intervals are required when creating a new GenomicsDB workspace:

    At least one interval must be provided, unless incrementally importing new samples in which case specified intervals are ignored in favor of intervals specified in the existing workspace.

    Let me know if you have any other questions.

    Best,

    Genevieve

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