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GATK didn't Output the InDel I expected
Hi! I used GATK to call InDel and SNP with my sequence data. But GATK didn't give any output variations(InDel and SNP).
So, I use GATK to generate a "bamout file" showing how HaplotypeCaller has remapped sequence reads(-disableOptimizations -forceActive -dt NONE).
The bottom bam file is the Input bam file and the top bam file is the HaplotypeCaller has remapped bam. I've checkd the base quality and mapping quality and there was no problem.
Why did GATK this remaping ? And Is this a bug?