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Hi, was this resolved? I'm having a similar problem: [[email protected] gatk]$ java /home/mpw6/GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar -T RealignerTargetCreator -R human_g1k_v37.fasta -I F03-03.sorted.nodup.bam -known 1000G_phase1.in…
After some time working on analysis for our Nature paper, I have returned my focus to this issue and have results to discuss. Using the default arguments with ReduceReads and using the resulting BAM as input to UnifiedGenotyper, I get a result set t…
Ok, that leads to a question I had earlier but never posted. It it really outside the scope of this thread, but since you mentioned GATK combining BAMs, I stumbled when I got to the VariantAnnotator since that didn't support multiple BAMs.