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

broadinstitute.org | 6 months ago
tip
Click on the to mark the solution that helps you, Samebug will learn from it.
As a community member, you’ll be rewarded for you help.
  1. 0

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

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

    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