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Nalini Ganapati

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Latest activity by Nalini Ganapati
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    Nalini Ganapati commented,

    1. Community
    2. Germline
    3. gatk GenotypeGVCFs produced an error

    Another thing, you may also need to invoke GenotypeGVFs with the --genomicsdb-shared-posixfs-optimizations if your workspace is on NFS/Lustre.

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    Nalini Ganapati commented,

    1. Community
    2. Germline
    3. gatk GenotypeGVCFs produced an error

    For 1000 WGS, partitioning by chromosome might be very resource intensive for both import and querying and you may have to partition your intervals with lesser granularity(e.g chr22:1-10000) if pos...

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    Nalini Ganapati commented,

    1. Community
    2. Somatic
    3. Mutect2 PoN - GenomicsDBImport creates empty DB

    Using GenomicsDBImport on the test vcf provided threw the following exception %: ./gatk --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' GenomicsDBImport -L 1:883600-883650 -V ex001.mutec...

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    Nalini Ganapati commented,

    1. Community
    2. Germline
    3. Strategy for buildling GenomicsDB

    Hi Bernt, From the gatk docs for GenomicsDBImport, --reader-threads is for reading vcfs only. For the import itself, you will have to use the --max-num-intervals-to-import-in-parallel option. Of co...

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