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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.

Reduce Reads error

I recently upgraded from GATK 2.5 to the latest 2.74 stable release, but the Reduce Reads throws the following error when I try to run it with a Bam file that was produced by "PrintReads" (3 samples merged in one Bam file).

MESSAGE: Bad input: Reduce Reads is not meant to be run for more than 1 sample at a time except for the specific case of tumor/normal >pairs in cancer analysis

java -Xmx6g -Djava.awt.headless=true -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T ReduceReads \ -R ../GATK_ref/hg19.fasta \ -I ../GATK/BQSR/all3Samples2.recal.bam \ -o ../GATK/BQSR/all3Samples.recal.compressed.bam

It used to work with the old version of GATK, but it does not work now. Where could it be wrong?



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @rcholic,

    The error message tells you why it is not working. The fact that it worked before is because we had not yet built in safety measures to prevent people from doing what you are trying to do.

  • Hi @Geraldine_VdAuwera

    I was wondering if you could confirm where the ReduceReads walker looks to determine if a bam is composed of 2 or more disparate samples. I presume it looks at the SM field for each of the read groups?

    I've pushed quite a few bams through our analysis workflow and there are a couple hundred that fail due to the above error. All of the reads are in from the same individual, but it appears the sequencing center that generated the data was not consistent with their SM fields in the read groups (some are full sample names and some are abbreviated). Assuming a user is certain that all reads are from the same individual/sample, would a simple solution be to specify the -cancer-mode flag (rather than re-header)?

    Thanks for your help.

  • Yes, all the GATK tools that operate on the sample level use the SM field. I have no idea if the cancer-mode flag will do what you want, but you absolutely need to fix your bams. Even if you can hack through this step, you'll get more problems in variant calling, and will face an absolute nightmare in the future if you ever come back to this data and "a couple hundred" bams are wrong. It will be well worth your time now to fix the bams and have everything just work. I would also keep a record of exactly what I changed in which files, just in case you ever need to troubleshoot

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @jpitt, you should definitely fix things so that the read groups, sample info etc are all correct and consistent -- preferably from the start of your pipeline. Using the cancer mode flag is not the right way to deal with this.

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