The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

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?


Issue · Github
by Sheila

Issue Number
Last Updated


  • SheilaSheila Broad InstituteMember, Broadie, Moderator


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


  • 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

    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

    @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.

Sign In or Register to comment.