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Negative read counts in Picard QualityYieldMetrics

vdhankanivdhankani USMember Posts: 3

Are negative values expected for TOTAL_READS, PF_READS and READ_LENGTH in QualityYieldMetrics? I'm guessing not. How I can track down the cause of this error then?


Issue · Github
by Sheila

Issue Number
Last Updated


  • SheilaSheila Broad InstituteMember, Broadie, Moderator, Dev Posts: 4,583 admin


    Hmm. Can you please tell us more about your data? How was it generated, and what pre-processing steps have you done?


  • vdhankanivdhankani USMember Posts: 3

    These are TCGA WGS bam files. We used them as-is, no pre-processing involved.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    Are you using a recent version of Picard? Can you please post your command line?

    Geraldine Van der Auwera, PhD

  • vdhankanivdhankani USMember Posts: 3
    edited August 2016

    the output of 'java -jar picard.jar BamIndexStats --version' is 2.1.0 .

    and here's the relevant bash script

    mkdir tmp
    if [[ ! -z ${OUTPUT_PREFIX+x} ]]; then
    java -jar /usr/picard/picard.jar CollectMultipleMetrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true INPUT=$INPUT_FILENAME OUTPUT="${OUTPUT_PREFIX}${INPUT_FILENAME}.multiple_metrics" PROGRAM=CollectInsertSizeMetrics PROGRAM=CollectQualityYieldMetrics PROGRAM=QualityScoreDistribution TMP_DIR=`pwd`/tmp
    java -jar /usr/picard/picard.jar BamIndexStats VALIDATION_STRINGENCY=LENIENT INPUT=$INPUT_FILENAME TMP_DIR=`pwd`/tmp > "${OUTPUT_PREFIX}${INPUT_FILENAME}.bamIndexStats.tsv"
    Post edited by Geraldine_VdAuwera on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    @vdhankani Can you please try the latest version (2.6) and see if the issue persists? If it does we would need a snippet of data to reproduce the error for local debugging.

    And I realize you said it's TCGA data so that could be complicated. sigh If you send us an identifier, we can get one of our devs with TCGA access to troubleshoot this. That might take a while though.

    Meanwhile you can try running ValidateSamFile in summary mode to check if there's anything wrong with the file. Even if it's TCGA data there could be errors in the file.

    Geraldine Van der Auwera, PhD

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