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Negative read counts in Picard QualityYieldMetrics

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?

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Issue · Github
by Sheila

Issue Number
1179
State
open
Last Updated
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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @vdhankani
    Hi,

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

    Thanks,
    Sheila

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

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

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

  • vdhankanivdhankani USMember
    edited August 2016

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

    and here's the relevant bash script

    #!/bin/bash
    
    # REQUIRED ENVIRONMENT VARIABLES:
    # - INPUT_FILENAME
    #
    # OPTIONAL ENVIRONMENT VARIABLES:
    # - OUTPUT_PREFIX
    #
    # CONTAINER IMAGE: b.gcr.io/isb-cgc-public-docker-images/qctools
    
    mkdir tmp
    
    if [[ ! -z ${OUTPUT_PREFIX+x} ]]; then
        OUTPUT_PREFIX="${OUTPUT_PREFIX}-"
    fi
    
    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

    @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.

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