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Analysis of somatic allele frequency

Good morning to all of you,

We have used GATK4 Mutect 2 to call somatic mutations from a customised NGS panel. However, we have problems regarding the mutant-allele percentage given by Mutect2. As a matter of fact, a patient harboring the V600E mutation in BRAF determined both by Sanger and a commercial NGS panel (Tumor 15, from Illumina), was found to have a % of mutant-allele of 0.4% after performing Mutect2. Moreover, this percentage does not fit with what we observed in the merged tumor bam files (around 24% of mutant-allele clone).

Could you please help us to tackle this problem?

Thank you so much.
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