The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?