We have a known SNV with AF ~1% and are trying to use Mutect2 to detect it in amplicon sequencing data.
- It can be called with no problem in some samples but cannot be called in other samples.
- The reads support ~1% AF for the SNV when examining input bam files.
- When running in debug mode, the log revealed that the region is not considered active and the variant was not called by Mutect2.
- The variant can be called with no problem with --force-active on.
We wonder how we can call the expected SNV in all samples consistently. One way we are thinking is to adjust active threshold. We also tried to examine activity profile but somehow --activity-profile-out is not available in GATK 188.8.131.52.
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