The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
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?