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Why is haplotype caller ignoring some reads and calling 1/1 variants instead of 0/1?
I compared the bam output from BWA-MEM and the bam output from HaplotypeCaller and I could see that for a specific active region GATK ignored some reads. Because of that, some variants were not called and others were called as homozygous instead of heterozygous. Could you please help me to understand why during the realignment step GATK does not consider the reads? I have checked mapping quality and alignment score and everything is ok. I am using GATK v4.
Thanks in advance.