HaplotypeCaller calling mutations based on one read?
I'm using GATK HaplotypeCaller, via grenepipe, with the default options as specified by grenepipe except for -ploidy 1 as I am working with haploid yeast. I am seeing some mutations called based on one single read only if I am interpreting the VCF correctly. Is this normal behavior? I would have thought the confidence would be too low to call a mutation based on one read?
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