I have whole-exome sequencing data of an immortalised non-tumor (normal) cell line that I wish to assess for the presence/absence of APC/Wnt mutations. This is to double check that the cell line is sufficiently "clean", without mutations in key regions, for further experimental analysis.
I understand that without a matched normal sample, I won't be able to distinguish if a variant is a somatic variant or a rare inherited germline mutation. As I just want to check for mutations in those regions, it is not important to distinguish between these types.
Question: Should I use the GATK haplotypecaller or a somatic variant caller such as Mutect2 without a matched-normal sample?