The variant in the end of a haplotype was missed.
The VAF of the missed variant is about 18% (59/330).
The other variants with similar VAF were called, so low VAF doesn't seem to be the reason.
How to make Haplotypecaller call the variant?
bam file (NGB_HLA-DQB1.zip) has been uploaded.
Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.
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