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Geert Vandeweyer

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Recent activity by Geert Vandeweyer Sort by recent activity Recent activity Votes

  • haplotycaller --alleles : arrayIndexOutofBoundsException

    1. Community
    2. Germline

    When running gatk 4.4.0.0 , I get an error for re-genotyping (--alleles) a 175bp deletion : command:  gatk --java-options "-Djava.io.tmpdir=/tmp -Xmx3g" HaplotypeCaller -R /home/gvandeweyer/AWS/hg1...

    • Geert Vandeweyer
    • 5 followers
    • 11 comments
    • 0 votes

  • Haplotypecaller 4.5.2.0 --alleles unexpected output

    Answered
    1. Community
    2. Germline

      - Output VCF file contains entries like below when '--alleles' is used: chr5    125894866       .       C       T       Infinity        .       AC=0;AF=0.00;AN=2;DP=31;ExcessHet=0.0000;FS=0.000;M...

    • Geert Vandeweyer
    • 2 followers
    • 7 comments
    • 0 votes