Which type of variant caller should I use in a WES normal cell line sample?
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12 months ago
bompipi95 ▴ 150

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?

variant-caller WES • 437 views
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Entering edit mode
12 months ago
ATpoint 83k

Any variant caller will do. Somatic calling is usually an additional mode while calling without matched normal is typically always possible.

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