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GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

DenverPosts: 68

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?

Tagged:

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.

Geraldine Van der Auwera, PhD

• Posts: 7

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)?