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Unified Genotyper gets stuck
I used bwa to map my samples to a mitochondrial genome of a non-model organism. Afterwards I careated a merged .bam file from multiple (288) sample .bams (used samtools merge and re-assigned RG tags), but when I run UnifiedGenotyper on that file it gets stuck at 32.1% and never moves forward from there. I also wanted to run RealignerTargetCreator, but I always get a truncated realigned.bam file. Any suggestions for how to troubleshoot this?