We have a known variant with high AF (~0.3) and are trying to use Mutect2 to detect it.
- It can be called with no problem if we disable subsampling with "--max-reads-per-alignment-start 0".
- The variant can be called with many non-zero values of --max-reads-per-alignment-start, such as 4000 and 16000.
- However, the variant is NOT called under certain values of --max-reads-per-alignment-start, such as 12000, despite the variant region having high depth (>30,000).
- When we enabled forced calling with "--max-reads-per-alignment-start 12000", it turned out that the subsampling only picked 5 reads for the base as the vcf sample field shown below.
We suspect that it might be due to some problems in subsampling step that the site is not covered as expected and would like to get feedbacks on how to resolve it.
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