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Hi. I am getting VERY odd results with some Streptococcus equi sequence. The BAM files from BWA align well in IGV, but when I run them through your pipeline there are many local errors where it seems that a single indel has been incorrectly multiplied up - somehow. You need to see the IGV screenshot.!
The bottom is a BAM file from BWA and the top is the final one from the GATK pipeline.