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ulitskyi

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  • Spurios indel

    1. Community
    2. Germline

    REQUIRED for all errors and issues: a) GATK version used: 4.3.0b) Exact command used: java -Xmx6g -jar gatk-package-4.3.0.0-local.jar HaplotypeCaller   -R hg19.fa -L dummy.bed -mbq 15  -G StandardA...

    • ulitskyi
    • 3 followers
    • 1 comment
    • 0 votes

  • HaplotypeCaller fails at regions of high depth

    1. Community
    2. General Discussion

    I'm looking a region from a targeted sequecing run. It is sequenced at high depth (~60K). If only 10,000 or even 40,000 reads per alignment start are used, there is no problem, and the region is ca...

    • ulitskyi
    • 6 followers
    • 15 comments
    • 0 votes