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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?