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MatZ

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  • bwa index doesn't create .alt file in hg38

    Answered
    1. Community
    2. Somatic

    We are using Gatk 4.1.4.1 to call somatic variant in the only tumor mode in hg38. We performed sequencing through an amplicon-based targeted gene panel. Due to the presence of another copy of a gen...

    • MatZ
    • 3 followers
    • 8 comments
    • 1 vote

  • How to keep MAPQ on multiple mapping reads

    1. Community
    2. General Discussion

    We are using Gatk 4.1.4.1 to call somatic variant in the only tumor mode in hg38. We performed sequencing through an amplicon-based targeted gene panel.   We are not able to call variants validated...

    • MatZ
    • 2 followers
    • 1 comment
    • 0 votes