org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?

broadinstitute.org | 2 months ago
  1. 0

    BaseRecalibrator: Array length mismatch detected. Malformed read — GATK-Forum

    broadinstitute.org | 2 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?
  2. 0

    BaseRecalibrator: Array length mismatch detected. Malformed read — GATK-Forum

    broadinstitute.org | 2 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?
  3. 0

    GATK | GATK | Tagged #bug

    broadinstitute.org | 6 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?
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  5. 0

    BaseRecalibrator: Array length mismatch detected. Malformed read — GATK-Forum

    broadinstitute.org | 2 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?
  6. 0

    Unified Genotyper Error - GATK-Forum

    broadinstitute.org | 8 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Alignment 8358067 | 20M1I36M87S

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    Root Cause Analysis

    1. org.broadinstitute.sting.utils.exceptions.ReviewedStingException

      Array length mismatch detected. Malformed read?

      at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateFractionalErrorArray()
    2. org.broadinstitute.sting
      BaseRecalibrator.map
      1. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateFractionalErrorArray(BaseRecalibrator.java:371)
      2. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:246)
      2 frames