Entering edit mode
3.2 years ago
ben83
▴
50
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?
