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Variant in VCF of multiple samples called by HaplotypeCaller absent in their respective BAM files
Hello GATK team,
I followed GATK best practices and called variants with haplotypecaller in 6 exome samples. However, in 4 patients (total) I have a variant on Chr12 that is absent in the BAM file. the variant is a big deletion (bigger than 10 nucleotides) and ONLY in one read of one of the samples I can see the variant. I'm confused about what has happened here. Can you please explain how can a variant be called while not present in the BAM?