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rcorbett

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Recent activity by rcorbett Sort by recent activity Recent activity Votes

  • GATK-DRAGEN standalone pipeline?

    Answered
    1. Community
    2. General Discussion

    Hi folks, I have been asked to try out your GATK-dragen pipeline.   I found this and related pages: https://gatk.broadinstitute.org/hc/en-us/articles/4411716682011-Full-release-of-open-source-DRAGE...

    • rcorbett
    • Edited
    • 5 followers
    • 7 comments
    • 0 votes

  • CollectRnaSeqMetrics GL000220 test not counting ribosomal reads

    Answered
    1. Community
    2. Other

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: gatk-4.1.9.0 b) Exact command used: gatk-4.1.9.0/gatk CollectRnaSeqMetrics -I A56781.STAR.genome.sorted.bam.dup.bam.chrU...

    • rcorbett
    • 2 followers
    • 5 comments
    • 0 votes

  • filterSamReads stdout format error

    1. Community
    2. Other

    Hi there, I am seeing some differences between the /dev/stdout and -O output.bam output formats for filterSamReads. GATK version:   gatk-4.0.10.0 Command 1: gatk-4.0.10.0/gatk FilterSamReads -I inp...

    • rcorbett
    • Edited
    • 2 followers
    • 15 comments
    • 0 votes